Method of identifying antibacterial compounds

ABSTRACT

The present invention relates to peptides having eubacterial b protein-binding properties and the surface of b protein with which said peptides and other proteins interact. The invention provides in vitro and in vivo assays for identifying compounds that modulate the interaction between b protein and proteins that interact therewith, and a method of controlling eubacterial infestation by modulating this interaction. The disclosed peptides can be used as templates for the design or selection of compounds that modulate the foregoing interaction.

TECHNICAL FIELD

[0001] The invention described herein in general relates to bacterialreplication. More specifically, the invention relates to compoundsuseful as inhibitors of bacterial replication. In particular, theinvention relates to a method of identifying compounds useful asinhibitors of bacterial replication, the compounds so identified, anduse of the compounds as antibacterial agents in the treatment orprevention of disease in humans, animals and plants.

BACKGROUND ART

[0002] Diseases due to bacterial infections of humans continue to causesuffering and economic loss despite the availability of antibacterialagents. Bacterial diseases of animals similarly cause suffering toafflicted animals and economic loss in instances where the diseasedanimals are of agricultural value. Although hundreds of differentantibacterial compounds are known, there is a continual need foralternative, more efficacious compounds. This is particularly so sincebacterial strains that are resistant to existing antibacterial agentshave emerged. In addition to identifying new antibacterial agents, it isdesirable to identify classes of compounds whose modes of action aredifferent to known classes of compounds. By identifying a class ofcompounds with a new mode of antibacterial activity, the armoury ofagents that can be used against bacterial disease is greatly enlarged.

[0003] Each form of life must duplicate its genetic material topropagate. Consequently, a potentially useful mode of action forantibacterial agents would be by interference with the duplication, orreplication, of the target bacterium's genetic material. The replicationof bacterial genetic material (DNA) is reasonably well understood andnumerous proteins are known to be involved: see the review by A.Kornberg et al., in DNA Replication, Second Edition, pp. 165-194, W. H.Freeman & Co., New York, 1992. During replication, most of theseproteins are organised into a complex multifunctional machine referredto as “the replisome”.

[0004] In eubacteria, the central enzyme of the replisome is DNAPolymerase III holoenzyme. In Escherichia coli (E. coli) this enzymecontains 10 different subunits, whilst in most other bacteria only sevensubunits have been identified. In E. coli, and probably in most othereubacteria, the DnaE orthologue (α subunit) is the main replicativepolymerase, but in many gram positive organisms a distinct, but relatedenzyme, PolC is proposed to be the main replicative enzyme replacingDnaE in the replication machine. The processivity of the replisome isconferred by the β subunit of DNA Polymerase III, which forms a clamparound the DNA. The β subunit is loaded as a homodimer onto DNA by aclamp loader complex comprising single subunits of δ and δ′ and foursubunits of τ/γ. All eubacteria studied to date contain genes encodingorthologues of the DnaE, β, δ, δ′ and τ/γ subunits of DNA Polymerase IIIand in E. coli these subunits have been shown to be essential for DNAreplication.

[0005] The β dimer, which encircles the DNA, but does not actually bindto it, confers processivity on DNA Polymerase III by maintaining theclose proximity of the DnaE or PolC subunits to the DNA. It has recentlybeen proposed that β may also act as an effector that increases theintrinsic rate of DNA synthesis (see Klemperer et al., J. Biol. Chem.(2000) 275: 26136-26143). In addition to DnaE, three other DNApolymerases present in E. coli (all of which are regulated by the LexArepressor protein) appear to interact with β. PolB (PolII) is involvedin DNA repair and the addition of β and the clamp loader complex leadsto an increase in enzyme processivity in in vitro assays (Hughes et al.,J. Biol. Chem. (1991) 267: 11431-11438). The addition of β and the clamploader complex to DNA Polymerase IV (DinB) does not increase theprocessivity of DNA synthesis, rather it dramatically increases theefficiency of synthesis (Tang et al., Nature (2000) 404:1614-1018). Theβ subunit appears to play a similar role in the activity of DNAPolymerase V, the UmuD′2UmuC complex (Tang et al., 2000).

[0006] While the site on β to which the δ and α subunits of E. coli DNApolymerase III bind has been studied in some detail, the nature of thesite(s) on δ, α and the other proteins that interact with β is notknown. Experimental evidence shows that at least some β-binding proteinscan interact productively with β proteins from heterologous species. Forexample, Staphylococcus aureus, Streptococcus pyogenes and Bacillussubtilis PolC subunits can use E. coli β as their processivity subunit(Low et al., J. Biol. Chem. (1976) 251: 1311-1325); Bruck and O'Donnell,J. Biol. Chem. (2000) 275: 28971-28983); Klemperer et al., 2000). Incontrast, E. coli DnaE cannot use β from the other species (Klemperer etal., 2000), the Helicobacter pylori δ subunit does not bind to E. coliβ, E. coli clamp loading complex cannot load S. aureus β (Klemperer etal., 2000) and the Streptococcus pyogenes clamp loading complex cannotload E. coli β P (Bruck and O'Donnell, 2000). These findings indicatethat there is a degree of specificity in the interaction of otherreplisome proteins with β.

[0007] For an antibacterial agent to be of use, it must have limitedactivity against at least eukaryotes so that it does not have an adverseeffect on the infected host, human or animal. In some circumstances, itis desirable that the antibacterial has activity against a limited rangeof bacteria such as a particular genus. The finding that there isspecificity in the interaction of eubacterial replisome proteins with βprotein raises the possibility that the interaction can be exploited asa mode of action of antibacterial agents with selectivity for members ofthe eubacteria.

SUMMARY OF THE INVENTION

[0008] The primary object of the invention is to provide a method ofidentifying new antibacterial agents with selectivity for members of theeubacteria. Other objects of the invention will become apparent from areading of the following summary and detailed description.

[0009] In a first embodiment, the invention provides a moleculecomprising a surface analogous to the surface of the domain ofeubacterial β protein contacted by proteins that interact with βprotein, wherein said surface is defined by the residues X¹⁷⁰, X¹⁷²,X¹⁷⁵, X¹⁷⁷, X²⁴¹, X²⁴², X²⁴⁷, X³⁴⁶, X³⁶⁰ and X³⁶², wherein thesuperscript numbers designate the position of residues in Escherichiacoli β protein, or the equivalent residues in homologues from otherspecies of eubacteria, and wherein:

[0010] X¹⁷⁰is any one of V, I, A, T, S or E;

[0011] X¹⁷² is any one of T, S or I;

[0012] X¹⁷⁵ is any one of H, Y, F, K, I, Q or R;

[0013] X¹⁷⁷ is any one of L, M, I, F, V or A;

[0014] X²⁴¹ is any one of F, Y or L;

[0015] X²⁴² is any one of P, L or I;

[0016] X²⁴⁷ is any one of V, I, A, F, L or M;

[0017] X³⁴⁶ is any one of S, P, A, Y or K;

[0018] X³⁶⁰ is any one of I, L or V; and

[0019] X³⁶² is anyone of M, L, V, S, T or R.

[0020] In a second embodiment, the invention provides a method ofidentifying a modulator of the interaction between a eubacterial βprotein and proteins that interact therewith, the method comprising thesteps of:

[0021] (a) forming a reaction mixture comprising:

[0022] (i) a ligand for eubacterial β protein that binds to at leastpart of the surface of β protein as defined in the first embodiment;

[0023] (ii) an interaction partner for said ligand; and

[0024] (iii) a test compound;

[0025] (b) incubating said reaction mixture under conditions which inthe absence of said test compound allows interaction between said ligandand said interaction partner; and

[0026] (c) assessing the effect of said test compound on saidinteraction between said ligand and said interaction partner.

[0027] In a third embodiment, the invention provides a method for the invivo identification of a modulator of the interaction between aeubacterial β protein and proteins that interact therewith, the methodcomprising the steps of:

[0028] (a) modifying a host to express or contain:

[0029] (i) a ligand for eubacterial β protein that binds to at leastpart of the surface of β protein as defined in the first embodiment; and

[0030] (ii) an interaction partner for said ligand;

[0031] (b) administering a test compound to said host and incubating thehost under conditions which in the absence of said test compound allowsinteraction between said ligand and said interaction partner; and

[0032] (c) assessing the effect of said test compound on saidinteraction between said ligand and said interaction partner.

[0033] In a fourth embodiment, the invention provides a method ofselecting a modulator of the interaction between a eubacterial β proteinand proteins that interact therewith, the method comprising the stepsof:

[0034] (a) establishing a consensus sequence for peptides that bind toat least part of the surface of β protein as defined in the firstembodiment;

[0035] (b) modelling the structure of at least a portion of saidconsensus sequence and searching compound databases for compounds havinga similar structure; wherein said modelling is by:

[0036] (i) searching protein databases for occurrences of said consensussequence or portion thereof, obtaining coordinates of residues ofproteins comprising said consensus sequence or portion thereof, andsuperimposing said coordinates to produce a pharmacophore model; or

[0037] (ii) modelling or determining the structure of a peptidecomprising said consensus sequence or a portion thereof when bound to βprotein; and

[0038] (c) testing compounds identified in step (b) for their effect onsaid interaction.

[0039] In a fifth embodiment, the invention provides a method ofreducing the effect of eubacterial infestation of a biological system,the method comprising delivering to a system infested with a eubacterialspecies a modulator of the interaction between eubacterial β protein andproteins that interact therewith.

[0040] In a sixth embodiment, the invention provides a template for thedesign of a compound that binds to at least part of the surface of βprotein as defined in the first embodiment, said template comprising apeptide selected from the group consisting of X¹X², X³X¹X², X³X¹X²X⁴,QX⁵X³X¹X², and QX⁵xX⁶X³X⁶, wherein: x is any amino acid residue; X¹ isL, M, I, or F; X² is L, I, V, C, F, Y, W, P, D, A or G; X³ is A, G, T,N, D, S, or P; X⁴is A or G; X⁵ is L; and, X⁶is L, I, V, C, F, Y, W or P.

[0041] The foregoing and other embodiments of the invention will bedescribed in detail below in conjunction with the drawings brieflydescribed hereafter.

BRIEF DESCRIPTION OF THE DRAWINGS

[0042]FIG. 1 is a schematic of the organisation of the domains of theDnaE and PolC subunits of the eubacterial DNA Polymerase III holoenzyme.

[0043]FIG. 2 gives results of a yeast two-hybrid experiments withLexA-β-binding motif protein fusions.

[0044]FIG. 3 gives structural alignments of amino acid sequences ofexamples of eubacterial δ proteins with sequences of E. coli δ′ and γ/τproteins. The sequences are designated as follows: tau/gamma, E. coli(Seq. ID No. 664); delta′, E. coli (Seq. ID No. 665); Ec, E. coli (Seq.ID No. 666); Rp, Rickettsia prowazekii (Seq. ID No. 667); Hp,Helicobacter pylori (Seq. ID No. 668); Mt, Mycobacterium tuberculosis(Seq. ID No. 669); B, Bacillus subtilis (Seq. ID No. 670); Mp,Mycoplasma pneumoniae (Seq. ID No. 671); Bb, Borrelia burgdorferi (Seq.ID No. 672); Tp, Treponema pallidum (Seq. ID No. 673); S, Synechocystissp. (Seq. ID No. 674); Cp, Chlamydiophila pneumoniae (Seq. ID No. 675);Dr, Deinococcus radiodurans (Seq. ID No. 676); Tm, Thermotoga maritima(Seq. ID No. 677); and Aa, Aquifex aeolicus (Seq. ID No. 678).

[0045]FIG. 4 gives the results of in vitro expression and interaction ofH. pylori DNA Polymerase III subunits.

[0046]FIG. 5 gives the results of experiments to test the interaction ofH. pylori DNA Polymerase III subunits in yeast two-hybrid assays.

[0047]FIG. 6 gives results for the expression of β-galactosidase inyeast two-hybrid assays.

[0048]FIG. 7 is a structural model of E. coli δ protein, showing theβ-binding region.

[0049]FIG. 8 gives the results of experiments to test the interaction ofnative and mutant E. coli δ subunits.

[0050]FIG. 9 is an analysis of the distribution of amino acids in thepentapeptide β-binding motif. A single peptide sequence with three ormore matches to the motif Qxshh (were ‘x’ is any amino acid, ‘s’ is anysmall amino acid and ‘h’ is any hydrophobic amino acid) in theappropriate region of the protein from each member of the PolC (22representatives included), PolB (15 representatives included), DnaE1 (72representatives included), UmuC (20 representatives included), DinB1 (62representatives included) and MutS1 (59 representatives included)families of proteins is included in the analysis. Percentage frequencyis plotted for each amino acid at each position of the pentapeptidemotif.

[0051]FIG. 10 gives the results of an experiment in which inhibition ofgrowth of B. subtilis by tripeptide DLF was tested.

[0052]FIG. 11 shows the three dimensional structure of E. coli β. Thelocation of the residues described in the first embodiment are indicatedby dark space-filled atoms.

DETAILED DESCRIPTION OF THE INVENTION

[0053] The one- and three-letter codes for amino acid residues inproteins and for nucleotides in DNA conform to the IUPAC-IUB standarddescribed in Biochemical Journal 219, 345-373 (1984).

[0054] The term “ligand” is used herein in the sense that it is acompound that binds to another compound, such as a protein, or to acell, by way of non-covalent bonds at a specific site of interaction.This meaning of the term is in accordance with its usage by, forexample, B. Alberts et al. in Molecular Biology of the Cell (GarlandPublishing, Inc, New York and London, 1983: seepage 127).

[0055] The term “interaction” is used herein to embrace the specificbinding of one molecule to another molecule without limitation as to thestrength of binding or the physical nature of the association.

[0056] The term “modulator” is used herein to denote a compound thateither enhances or inhibits the interaction between β protein and aligand therefor. Modulators are thus either agonists or antagonists ofthe interaction.

[0057] The present invention stems from the identification, in a broadrange of species of eubacteria, of a peptide motif responsible for thebinding of proteins involved in DNA replication and repair to the clampprotein, β. The identification of this motif has also allowedelucidation of the β protein domain responsible for the interaction withproteins that bind thereto. We teach herein the parameters for designingcompounds that inhibit the interaction of proteins with β. We also teachhow to develop simple reagents for facilitating the screening ofcompounds for inhibitory or stimulatory activity. In particular, thedevelopment of a wide range of simple and robust assay systems for highthroughput screening of natural products or synthetic compounds for suchactivity. From an understanding of the structures of the participants ofthe various protein-protein interactions involving the β protein and itsligands, new antibacterial agents with selective activity againsteubacteria can be designed and the activity—including inhibitory andstimulatory activity—of such compounds tested by methods to be describedin detail below. In addition, compounds are described with inhibitoryactivity in binding assays and with in vivo antibacterial activity.

[0058] The present inventors have established that peptides havingeubacterial β protein-binding properties comprise at least the dipeptideX¹X², wherein X¹ is L, M, I, or F, and X² is L, I, V, C, F, Y, W, P, D,A or G. Peptides advantageously comprise a tripeptide, a tetrapeptide, apentapeptide or a hexapeptide. Preferred dipeptides are X¹F wherein X¹is as defined above. Preferred tripeptides are X³X¹X² wherein X¹ and X²are as defined above and X³ is A, G, T, N, D, S, or P. Preferredtetrapeptides are X³X¹X²X⁴ wherein X¹, X² and X³ are as previouslydefined and X⁴ is A or G. Preferred pentapeptides are QX⁵X³X¹X² whereinX¹, X² and X³ are as above and X⁵ is L. Particularly preferredpentapeptides are QLxLxL. Preferred hexapeptides are QX⁵xX⁶X³X⁶ whereinx, X³ and X⁵ are as defined above and X⁶ is L, I, V, C, F, Y, W or P.

[0059] Particularly preferred specific pentapeptides are QLSLF (Seq. IDNo. 622), QLSMF (Seq. ID No. 623), QLDMF (Seq. ID No. 624) and QLDLF(Seq. ID No. 625). For Pseudomonads, the pentapeptides HLSLF (Seq. IDNo. 626), HLSMF (Seq. ID No. 627), HLDMF (Seq. ID No. 628) and HLDLF(Seq. ID No. 629) are advantageous. Particularly preferred tetrapeptidesare X³LFX⁴, wherein X⁴ is either A or G. Particularly preferredtripeptides are SLF, SMF, DLF and DMF. Particularly preferred dipeptidesare LF and MF. The examples below give further details of preferredpeptides.

[0060] The peptides set out above have utility as:

[0061] (i) reagents for the assay of modulators of the interactionbetween β protein and any ligand therefor;

[0062] (ii) inhibitors per se of the interaction between β protein andany ligand therefor;

[0063] (iii) templates for the design of molecules that modulate theinteraction between β protein and any ligand therefor; and

[0064] (iv) determining the surface of the binding domain on β proteinwith which ligands interact from which surface modulators of theinteraction can also be designed.

[0065] Peptides according to the invention can be synthesised and/ormodified (see discussion on mimetics below) by any of the methods knownto those of skill in the art. Alternatively, peptides can be excisedfrom larger polypeptides that include the desired peptide sequence. Thelarger polypeptide can be produced by recombinant DNA means, as can thepeptide per se.

[0066] With regard to the first embodiment of the invention as definedabove, the three dimensional structure of the binding surface of β isdefined by the co-ordinates of the residues specified above in thetertiary structure of E. coli β as described by Kong et al. (see Cell(1992) 69: 425-437).

[0067] Molecules including surfaces according to the first embodimenthave utility as:

[0068] (i) reagents for the assay of the interaction between β proteinand any ligand therefor;

[0069] (ii) modulators per se of the interaction between β protein andany ligand therefor;

[0070] (iii) templates for the design of molecules that inhibit theinteraction between β protein and any ligand therefor;

[0071] (iv) templates for modelling the structure of the of the bindingdomain on β protein from which structure modulators of the interactioncan also be designed;

[0072] (v) direct target sites for covalent and non-covalentinteractions with compounds; and

[0073] (vi) indirect target sites, wherein said site or part of the siteis obscured by compounds covalently or non-covalently bound elsewhere onβ or β-binding proteins, peptides or compounds.

[0074] Regarding the second embodiment, the ligand can be any entitythat binds to the β protein at the surface or part of the surfacedefined in the first embodiment or a mimetic of these domains orsurfaces of the β protein. The ligand can thus range from a simpleorganic molecule to a complex macromolecule, such as a protein. Typicalprotein ligands include, but are not limited to, δ, DnaE1, DnaE2, PolC,PolB2, UmuC, DinB1, DinB2, DinB3, MutS1, RepA, Duf72 and DnaA2, andfragments thereof that are responsible for the interaction with βprotein. Ligands also include the peptides defined above and mimetics ofthe peptides derived from β-binding proteins fused in whole or in partto other proteins, such as LexA, GST or GFP, peptides derived fromβ-binding proteins fused to other proteins such as LexA, GST or GFP,peptides as defined above that bind to eubacterial β proteins, butderived from proteins that do not themselves bind to β. Ligands alsoinclude antibodies and related molecules, such as single chainantibodies, that bind in whole or in part at or near to the surface of βprotein as defined above in the first embodiment of the invention.

[0075] In the context of the present invention, the term “mimetic” of apeptide includes a fragment of a protein, peptide or any chemical formthat provides substituents in the appropriate positions to enable thebinding of compounds, in whole or in part, to the binding site on βprotein in the manner of the peptides identified above. Those of skillin the art will be aware of the approaches that can be for the design ofpeptide mimetics when there is little or no secondary and tertiarystructural information on the peptide. These approaches are described,for example in an article by Kirshenbaum et al., (Curr. Opin. Struct.Biol. 9:530-535 [1999]), the entire content of which is incorporatedherein by cross reference. Approaches that can be taken include thefollowing as examples:

[0076] 1. Modification of the amino acid side chains to increase thehydrophobicity of defined regions of the peptide. For example,substitution of hydrogens with methyl groups on the phenylalanine atposition 5 of the pentapeptide.

[0077] 2. Substitution of the side chains with non-amino acids. Forexample, substitution of the phenylalanine at position 5 of thepentapeptide with other aryl groups.

[0078] 3. Substitution of the amino- and/or carboxy-termini with novelsubstituents. For example, aliphatic groups to increase thehydrophobicity of the tripeptide DLF.

[0079] 4. Modification of the backbone (amide bond surrogates), forexample replacement of the nitrogens with carbon;

[0080] 5. Modification of the backbone to introduce steric constraints,such as methyl groups.

[0081] 6. Peptoids of N-substituted glycine residues.

[0082] 7. Substitution of one or more L amino acids in the peptidesequences with D amino acids.

[0083] 8. Substitution of one or more α-amino acids in the peptidesequences with β-amino acids or γ-amino acids.

[0084] 9. Retro-inverso peptides with reversed peptide bonds and D-aminoacids assembled in reverse order with respect to the original sequence.

[0085] 10. The use of non-peptide frameworks, such as steroids,saccharides, benzazepine 1,3,4-trisubstituted pyrrolidinone, pyridonesand pyridopyrazines and others known in the art.

[0086] 11. The insertion of spacer amino acids. For example, to generatepeptides of the form X¹X⁵X², QxX³X¹X⁵X² and QL X³X¹X⁵X² where X¹ is L,M, I or F, X² is L, I, V, C, F, W, P, D, A or G, X³ is D or S, and X⁵ isA, S, G, T, D or P. Particularly preferred hexapeptides containing thismotif are shown in Table 13. A hexapeptide is in effect a “natural”mimetic of a pentapeptide with a single amino acid-residue spacer.

[0087] 12. The use of approaches 1 to 10 with the peptides described at11.

[0088] The interaction partner of the second embodiment includes thefollowing compounds:

[0089] (i) a eubacterial β protein per se, or at least a portion of thedomain thereof that includes at least a functional portion of thesurface of the domain as defined in the first embodiment;

[0090] (ii) a mimetic of the interaction partner as defined in (i);

[0091] (iii) a peptide as defined above, or a polypeptide including atleast one copy of the foregoing peptide; and

[0092] (iv) a compound that binds to the peptide of (iii).

[0093] With regard to a mimetic of item (ii) of the preceding paragraph,this can comprise a conformationally constrained linear or cyclicpeptide that folds to mimic the disposition of the side chains of theamino acids in the native β protein or linked linear peptidesrepresenting in whole, or part, the discontinuous peptides comprisingthe surface. Conformational constrains may be obtained using disulphidebridges, amino acid derivatives with known structural constraints,non-amino acid frameworks and other approaches known to those skilled inthe art, (Fairlie et al., Current Medicinal Chemistry (1998) 5:29-62,Stigers et al., Current Opinion in Chemical Biology (1999) 3:714-723).The mimetics can be antibodies, and related molecules, such as singlechain antibodies, that bind in whole or in part to the peptides definedabove, or mimetics of these peptides. The mimetics can comprise aprotein engineered to express this site or region of β, or any chemicalform that provides substituents in the appropriate positions to mimicside chains of the residues making up the peptides. These molecules caninclude modifications as described in 1-12 above.

[0094] In addition to the designed structural mimetics of theinteracting peptides and the surface of β as described above, othermimetics can also be designed or selected. These include compounds thatbind to the peptides defined above, including those designed/identifiedby structural modelling/determination of the peptides, the proteins inwhich they occur, or of eubacterial δ proteins. Also included arecompounds that bind to β and occupy or occlude (in whole or in part) thestructural space defined by the published co-ordinates in the 3Dstructure of E. coli β (Kong et al., Cell (1992) 69: 425-437) of theamino acid residues identified in the second embodiment or by modellingand/or structural determination of the equivalent positions in theorthologues of β from other species of eubacteria. Such mimetics maymimic the function, but not necessarily the structure of the peptides.Such mimetics could be identified by methods including screening ofnatural products, the production of phage display libraries (Sidhu etal., Methods in Enzymology (2000) 328:333-363), minimized proteins(Cunningham and Wells, Current Opinion in Structural Biology (1997)7:457-462), SELEX (Aptamer) selection (Drolet et al., Comb. Chem. HighThroughput Screen (1999) 2:271-278), combinatorial libraries andfocussed combinatorial libraries, virtual screening/database searching(Bissantz et al., J. Med. Chem. (2000) 43:4759-4767) and rational drugdesign as known to those skilled in the art (Houghten et al., DrugDiscovery Today (2000) 5:276-285). Such combinatorial libraries could bebased on the peptide sequences—or their preferred forms as set outabove—subjected to combinatorial variation as known to a medicinalchemist skilled in the art, or based upon the predictions of computerprograms used for drug design (for example components of the InsightIIand Cerius2 environments from MSI and the SYBYL Interface from Tripos).The libraries would be designed to include an adequate sampling of therange and nature of compounds likely to bind to β and occupy or occlude(in whole or in part) the structural space as defined above. For examplethe method of Erlanson et al., (Proc. Natl. Acad. Sci. (2000)97:9367-9372) utilising the Ser345Cys mutant of E. coli β as describedin example 9, or equivalent mutants of other eubacterial β proteins, totether compounds adjacent to the binding site on β could be combinedwith the combinatorial target-guided ligand assembly of Maly et al.,(Proc. Natl. Acad. Sci. (2000) 97:2419-2424) utilising, as an example,phenylalanine or the preferred dipeptides to efficiently nucleate thesynthesis of mimetics of the peptides.

[0095] Compounds that can be utilised as test compounds in the method ofthe second embodiment include the following:

[0096] (i) a peptide as defined above, or a polypeptide that includes atleast one copy of the peptide;

[0097] (ii) a mimetic of the peptide of (i);

[0098] (iii) a mimetic of at least part of the binding surface asdefined in the second embodiment that retains at least part of thebinding function of the whole surface;

[0099] (iv) a natural product or chemical compound that binds (i) or(ii);

[0100] (v) a natural product or chemical compound that binds in whole orin part to the binding surface of β protein as defined in the firstembodiment; and

[0101] (vi) any compound that binds to either or both of the ligand andthe interaction partner used in the assay.

[0102] It will of course be appreciated that when the ligand orinteraction partner is a mimetic of β protein or the binding surfacethereof and the test compound is also a mimetic of either entity, thesecond-mentioned mimetic will be a different molecule to the mimetic ofβ protein or the binding surface.

[0103] The method of the second embodiment can be carried out using anytechnique by which receptor-ligand interactions can be assayed. Forexample, surface plasmon resonance; assays in solution or using a solidphase, where binding is measured by immunometric, radiometric,chromogenic, fluorogenic, luminescent, or any other means of detection;any chromographic or electrophoretic methods; NMR, cryoelectronmicroscopy, X-ray crystallography and/or any combination of thesemethods.

[0104] Advantageously, in the method of the second embodiment, eithercomponent (i) or (ii) is immobilised on a solid support. The othercomponent can be labelled so that binding of that component to theimmobilised other component can be detected. Suitable labels will beknown to one of skill in the art, as will suitable solid supports.Typically, the label is a radioactive label such as ³⁵ incorporated intothe compound comprising either component (i) or (ii). Alternatively thecomponent in solution may be detected by binding of antibodies specificfor the component and suitable development known to one of skill in theart.

[0105] A typical procedure according to the second embodiment is carriedout as follows. In this procedure, the ligand for β protein is αprotein. The purified α subunit protein is adsorbed onto the wells of amicrotitre plate. The β subunit protein, with or without test compound,is added to the α adsorbed wells and incubated. The plate is washed freeof unbound protein, and incubated with antibody specific for the βsubunit. The bound antibody is then detected with a species specificIg-horseradish peroxidase conjugate and appropriate substrate. Thechromogenic product is measured at the relevant wavelength using a platereader.

[0106] Turning to the third embodiment of the invention, the ligand andinteraction partner can be any of the ligands and interaction partnersused in conjunction with the second embodiment that can be expressed,including transient expression, in a host cell. The cell does notnecessarily have to be genetically modified to express the ligand orinteraction partner, which entities can be introduced into the cellusing liposomes or the like. Advantageously, the ligand is a peptideselected from those defined above, a polypeptide including at least onecopy of such a peptide, or a mimetic of the foregoing compounds.Similarly, the interaction partner is a eubacterial β protein per se, orat least a portion of the domain thereof that includes at least afunctional portion of the surface of the domain as defined in the firstembodiment. The interaction partner is advantageously also a mimetic ofthe compounds specified in the previous sentence.

[0107] The modified host of the method of the third embodiment can be ananimal, plant, fungal or bacterial cell, a bacteriophage or a virus.Methods for modifying such hosts are generally known in the art and aredescribed, for example, in Molecular Cloning A Laboratory Manual (J.Sambrook et al., eds), Second Edition (1989), Cold Spring HarborLaboratory Press, the entire content of which is incorporated herein bycross-reference.

[0108] So that the inhibition or potentiation of the interaction betweenthe β protein and ligand can be easily assessed, the host isadvantageously engineered to include an indicator system. Such indicatorsystems are well known in the art. A preferred indicator system is theβ-galactosidase reporter system.

[0109] A preferred procedure for carrying out the method of the thirdembodiment is by the modification of the yeast two-hybrid assaysdescribed in Example 2 below. Compounds at appropriate concentrationsare added to the growth medium prior to assay of β-galactosidaseactivity. Compounds that inhibit the interaction of the β-bindingprotein with β will reduce the amount of β-galactosidase activityobserved.

[0110] With reference to the fourth embodiment of the invention, detailsof peptide sequences suitable for structure modelling are given herein.Those of skill in the art will be familiar with the modelling proceduresby which structures can be provided.

[0111] In step (b)(i) of the method of the fourth embodiment, theportion of the consensus sequence can be a tripeptide. A particularlypreferred tripeptide is DLF. In the step (b)(ii) method, thepentapeptide and hexapeptide sequences defined above are preferred.However, any of the peptides disclosed herein can be employed. The term“modelling” as used in the context of step (b)(ii) includes adetermination of the structure of a peptide when bound to the surface ofβ-protein.

[0112] The assay procedures described above can advantageously be usedin step (c) of the fourth embodiment method.

[0113] Regarding the fifth embodiment of the invention, the term“eubacterial infestation of a biological system” is used herein todenote: disease-causing infection of an animal, including humans;infection or infestation of plants and plant products such as seeds,fruit and flowers; infestation of foods and contamination of foodproduction processes; infestation of fermentation processes;environmental contamination by a eubacterial species such ascontamination of soil; and the like. The term should not be interpretedas limited to the foregoing situations, however, as the method isapplicable to any situation where reduction or elimination of the numberof a eubacterial species is desired.

[0114] Compounds used against a eubacterial infestation—that is,compounds that modulate the interaction between a eubacterial β proteinand proteins that interact therewith—are preferably inhibitors of thatinteraction. However, modulator compounds that enhance the interactionbetween a eubacterial β protein and proteins that interact therewith canalso be used against eubacterial infestations. In the lattercircumstance, the efficacy of the compound lies in it inhibiting therelease at the correct of a protein bound to β with disruption of cellreplication. DNA replication requires the exchange of proteins on β,primarily the α and δ proteins of the replisome.

[0115] The term “infested” as used in the fifth embodiment andthroughout the description embraces a systemic infection of eukaryoticorganisms, such as animal, plants, fungi and sponges or surfaceinfection thereof by a eubacterial species. The term also includesinfections of parts of eukaryotic organisms such as infection of meatand plant products. The term further embraces an infection of a cultureof microorganisms. The term further includes the presence of aeubacterial species in a process or on a surface in a physicalenvironment.

[0116] The term “delivering” as used in the fifth embodiment andthroughout the description embraces administering the inhibitor compoundin such a manner that it is taken up by a subject animal, plant ormicroorganism infested with a eubacterial species. In this context theterm includes applying the inhibitor compound to the infested surface orto an animal or plant although the inhibitor compound may notnecessarily need to be taken up by the organism if the eubacterialinfestation is limited to the surface thereof. The term also embracesgenetically modifying an animal, plant or microorganism so that theinhibitor compound is expressed endogenously by the modified organism.The genetic modification can include a mechanism for the regulatedexpression of the inhibitor compound. For example, a gene or genes forexpression of an inhibitor compound introduced into a plant can be underthe control of a promoter that is responsive to eubacterial infestationof the plant. Methods for genetically modifying an animal, plant ormicroorganism to express the desired inhibitor compound will be known tothose of skill in the art as will methods of controlling expression ofthe inhibitor compound. The term “delivering” further includes thephysical delivery of a composition including the inhibitor compound ontoa surface or into a physical environment such as by spraying, wiping orthe like.

[0117] The amount of modulator compound administered will depend on theparticular compound, the nature of the infested system, and theeubacterial species involved. Those of skill in the art of theapplication of antibacterials will be cognizant of the amount of aparticular inhibitor compound to use.

[0118] Modulator compounds are typically administered as compositionscomprising the compound and a suitable carrier substance. Compositionscan also include excipients, adjuvants and bulking agents, or any othercompound used in the preparation of pharmaceutical, veterinary andagricultural compositions, or compositions for environmental use.Compositions can also include additional active agents such as otherantibacterials or therapeutic agents.

[0119] Compositions can be prepared as syrups, lotions, sprays, tablets,capsules, gels, creams, or mere solutions. The nature of the compositionused, and the route of administration, will depend on the biologicalsystem subject to the infestation, and the nature of the infestation.For example, a eubacterial infection of a human would normally betreated by administration of tablets or capsules comprising acomposition of the modulator compound, or in more extreme cases byinjection of a solution containing a modulator compound.

[0120] Compositions can be prepared by any of the procedures known tothose of skill in the art. The invention also includes within its scopeuse of a modulator of the interaction between eubacterial β protein andother proteins for the preparation of a medicament for reducing theeffect of eubacterial infestation of a biological system.

[0121] As indicated above, the peptides of the invention can be used astemplates for the design of modulators of the interaction of ligandswith β protein. Such modulator compounds are advantageously mimetics ofthe peptide, as peptides or polypeptides may be prone to proteolyticdegradation by the target eubacterium or an infected host. Nevertheless,polypeptides and peptides may have use in some circumstances.

[0122] With regard to mimetics of the peptides and the surface of the βprotein, these can take any chemical form as described above.

[0123] It will be appreciated that efficacy of any designed modulatorcompound can be tested using the methods of the second or thirdembodiments. It will also be appreciated that the modulator compoundutilised in the fifth embodiment can be a designed modulator compound,or any compound, or mixture of compounds, identified as an efficaciousmodulator through use of the methods of the second and thirdembodiments.

[0124] Non-limiting examples of the invention follow.

EXAMPLE 1

[0125] In this example, we describe the identification of peptide motifsof replisomal proteins responsible for the interaction of the proteinswith the processivity clamp, β.

A. Methods

[0126] Analysis of Amino Acid Sequences

[0127] Alignments of amino acid sequences of the protein families wereconstructed by taking sequences from a number of sources. PSI-BLASTsearches of the non-redundant database of proteins at the NCBI, BLASTsearches of the unfinished and completed genomes at the followingservers:

[0128] NCBI(http://www.ncbi.nlm.nih.gov/Microb_blast/unfinishedgenome.html),

[0129] TIGR (http://www.tigr.org/cgi-bin/BlastSearch/blast.cgi?),

[0130] Sanger Center(http://www.sanger.ac.uk/DataSearch/omniblast.shtml), and

[0131] DOE Joint Genome Institute(http://spider.jgi-psf.org/JGI_microbial/html).

[0132] Searches of non-redundant GenPept and B. subtilis open readingframes were undertaken using the Pattinprot server(http://pbil.ibcp.fr/cgi-bin/npsa_automat.p1?page=npsa_pattinprot.html).Predicted secondary structures were determined using the followingservers:

[0133] PSIPRED at http://insulin.brunel.ac.uk/psipred), and

[0134] Jpred at http://jura.ebi.ac.uk:8888/submit.html.

[0135] Protein fold recognition was carried out using the 3D-PSSM serverv2.5.1 at http://www.bmm.icnet.uk/˜3dpssm. Modelling was carried outusing the SWISS-MODEL server athttp://www.expasy.ch/swissmod/SM_FIRST.html. Models were manipulatedusing SWISS-MODEL and the Swiss-PdbViewer.

B. Results

[0136] Eubacterial Polymerases DnaE, PolB and PolC Contain a ConservedPeptide Motif at the Carboxy-Terminus of their Polymerase Domains

[0137] The major eubacterial replicative polymerases, are the α subunitsof DNA Polymerase III (DnaE and PolC). Whilst PolB is a repairpolymerase, the carboxy-terminus of the eubacterial PolB proteinscontains the short conserved peptide QLsLF. Inspection of thecarboxy-termini of the members of the eubacterial PolC family of DNAPolymerases also identified a short peptide with the consensus sequenceQLSLF (Seq. ID No. 622) at, or very close to, the carboxy-terminus ofall members of the family so far identified. The results of thisanalysis are presented in Table 1 for the PolC1 family and in Table 2for the PolB2 family. In these tables, and the following tables ofsequence data, the residues comprising the motif are presented (secondlast column) as well as the ten residues on the N-terminal side of themotif, and up to the tenth residue on the C-terminal side of the motifwhere such residues occur. In both families the peptide is not predictedto be part of a helix or sheet and is predicted to be preceded by ahelix. Thus, this motif is a good candidate for a β-binding site in theeubacterial enzymes.

[0138] PolC is the α subunit of DNA Polymerase III in many gram-positivebacteria. However, in most bacteria DnaE is the α subunit. If thepeptide QLsLF were indeed part of the β-binding site it should also bepresent in the DnaE subunit. The members of the DnaE and PolC familiesare related and contain similar domains, but are organised in slightlydifferent ways (FIG. 1). The DnaE family can be further divided into theDnaE1 and DnaE2 subfamilies on the basis of their domain organisation(FIG. 1) and sequence similarities. Inspection of the carboxy-termini ofthe members of the DnaE1 and DnaE2 subfamilies did not identify anyconserved peptide motif similar to QLsLF. Detailed analysis of theregion immediately following the proposed helix-hairpin-helix domain(equivalent to the location of the QLsLF motif in the PolC enzymes)identified the short peptide with the consensus sequence QxsLF asequivalent to the motif identified in PolB and PolC. The data used forthis analysis are presented in Tables 3 and 4. Structures shown werepredicted using 3D-pssm with the E. coli DnaE1 sequenced used toinitiate the alignment of sequences. Sequence data shown for the speciesY. pestis, H. ducreyi, P. multocida, A. actinomycetemcomitans, S.putrefaciens, P. aeruginosa, P. putida L. pneumophila, T. ferroxidans,N. gonorrhoeae, B. brochiseptica, B. pertussis, R. sphaeroides, C.crescentus, D. vulgaris, G. sulfurreducens, M. leprae, M. avium, C.diptheriae, C. difficile, D. ethogenes, S. aureus, B. anthracis, E.faecalis, S. pneumoniae, S. pyogenes, C. acetobutylicum, T. denticola,C. tepidum and P. gingivalis, are preliminary data obtained from theunfinished genomes server at at the following NCBI site:

[0139] NCBI(http://www.ncbi.nlm.nih.gov/Microb_blast/unfinishedgenome.html).

[0140] Sequence data shown for the species N. europaea, E. faecium, R.palustris, P. marinus and N. punctiforme are preliminary data and wereobtained from relevant unfinished genomes servers at the DOE JointGenome Institute (http://spider.jgi-psf.org/JGI_microbial/html/).

[0141] In addition a small amino acid is favoured immediately precedingand following the central motif. The peptide is not predicted to be partof a helix or β-sheet and is predicted to be preceded by a helix.

[0142] Identification of a Peptide with the Consensus QLsLF in Membersof the UmuC/DinB Family of Repair Polymerases.

[0143]E. coli DNA Polymerases IV and V have increased efficiency of DNAsynthesis in the presence of β. The UmcC/DinB family can be furtherdivided into four subfamilies on the basis of sequence similarities. Thefour subfamilies have been designated DinB1, DinB2, DinB3 and UmuC.Analysis of the sequences of members of the DinB1 subfamily (PolymeraseIV) identified a somewhat conserved peptide motif (Table 5), with thevery loose consensus QxsLF at, or close to, the carboxy-terminus of theproteins. Polymerase V is a multi-subunit enzyme containing twomolecules of a cleaved version of UmuD, designated UmuD′ and UmuC, thepolymerase subunit. The members of the UmuC subfamily contained theconserved peptide motif, QLNLF (Seq. ID No. 630), approximately sixtyamino acids from the carboxy-terminus of the protein (Table 7). The UmuCsubfamily includes the chromosomally encoded UmuC proteins and theplasmid encoded SamB, RulB, MucB, ImpB and RumB proteins. Members of athird subfamily, DinB2, present in plasmids and bacteriophages of grampositive bacteria also contained a conserved motif with the sequenceQLSLF (Seq. ID No. 622) at the equivalent position to the motifs in theDinB and UmuC subfamilies (Table 6).

[0144] Identification of Putative β-Binding Sites in Proteins Involvedin Mismatch Repair

[0145] The MutS superfamily is common to mismatch DNA repair systemsacross the evolutionary landscape. The MutS protein is involved in theinitial recognition of mismatches. The MutS superfamily has been dividedinto two families, MutS1 and MutS2. In the eubacteria, singlesubfamilies of the MutS1 and MutS2 families have been identified. In theMutS1 family, a conserved peptide matching the β-binding motif wasidentified in most members of the family (Table 8). The motif lies in aregion of amino acid sequence polymorphic in length and sequence lyingbetween the conserved MutS domain and a short conserved domain specificto eubacteria at the carboxy-terminus of the proteins (Table 8). Thepeptide is not predicted to be part of a helix or sheet and is predictedto be preceded by a helix. Similar motifs were not identified in membersof the MutS2 superfamily.

[0146] Determination of β-Binding Peptide Consensus Sequence

[0147] The frequency of each amino acid at each position of the alignedproposed β-binding peptides was plotted (FIG. 9). From this plot, theconsensus sequence of the pentapeptide was determined to be QL[SD]LFwhere [SD] means either S or D (Seq. ID No's 582 and 584, respectively).

[0148] Other Eubacterial Proteins with Possible β-Binding Sites

[0149] The proposed β-binding sites have a number of common features;they are not in domains that are conserved across all members of a groupof families of proteins, they are usually at the carboxy-terminus of theprotein, they are in regions of variable amino acid sequence and length,they are in regions not predicted to be in helices or sheets, they arefrequently preceded by a helix and although the tertiary structures ofthese proteins are not known the peptides are likely to be on theexternal surface of the proteins. The non-redundant GenPept proteinsequence database was searched for proteins containing the sequenceQLSLF (Seq. ID No. 622) and the B. subtilis protein sequence databasewas searched for the peptide sequences related to QLSLF. Hits inproteins known to be involved in DNA replication and repair wereinvestigated in more detail.

[0150] The location and amino acid conservation of the peptide motif andof the flanking sequences and predicted secondary structure wereevaluated against the features above. With one exception, no furtherfamilies of proteins that met these criteria were identified. The oneexception was a number of proteins in a family of RepA proteins encodedby plasmids E. coli RA1, Acidothiobacillus ferrooxidans pTF5 andBuchnera aphidicola pBPS2 (Table 9).

[0151] Members of the fourth subfamily of the UmuC/DinB superfamily,DinB3, exhibited a much lower level of conservation of the motif, butwith a few exceptions the Q or LF parts of the motif were conserved(Table 10).

[0152] In addition, a probable β-binding site was identified at thecarboxy-terminus in some, but not all, members of the Duf72 family ofproteins of unknown function (Table 11). The Duf72 family (Pfam PF01904)is described at the following site:

[0153] Pfam (http://www.sanger.ac.uk/Software/Pfam/index.shtml)

[0154] and includes the E. coli YecE protein (NCBI gi:1788175) and theB. subtilis YunF protein (NCBI gi:2635736). Further members of thefamily were identified by BLAST searches of databases as described inthe methods section.

[0155] Analysis of a family of proteins related to DnaA, here designatedthe DnaA2 family and exemplified by the E. coli YfgE protein (NCBIgi:1788842), identified a probable β binding site at the amino-terminus(Table 12). Again, further members of the family were identified byBLAST searches of databases as described in the methods section above.

[0156] Identification of a Second, Hexapeptide, Putative β-Binding Motif

[0157] Analysis of the sequences of the proposed DnaA2 β-binding motifsuggested that a hexapeptide with the consensus sequence QLxLxh (where xis any amino acid and h is any hydrophobic amino acid) might constitutea second less common β-binding motif. Examples of a similar motif alsooccur at low frequency in some of the other families of proteins, as canbe appreciated from the data of Table 13. Overall, the sequences appearto have the loose consensus sequence QxxLxh. TABLE 1 PolC1 ProteinFamily Sequences Seq. ID Sequence No. Sequence name N-term Motif C-term553 122 PolC1 Thermotoga maritima MSB8 GVLGDLPETE QFTLF 554 415 PolC1Desulfitobacterium hafniense DCB-2 DCLKGIPESD QISFF DLIS 555 101 PolC1Clostridium difficile 630 GSLENMSERN QLSLF 556 229 PolC1Carboxydothermus hydrogenoformans GCLKGLAPTS QLVLF A TIGR 557 227 PolC1Bacillus halodurans C-125 GCLEGLPESN QLSLF 558 104 PolC1 Bacillusstearothermophilus 10 GCLDSLPDHN QLSLF 559 103 PolC1 Bacillus subtilis168 GCLESLPDQN QLSLF 560 105 PolC1 Staphylococcus aureus GSLPNLPDKAQLSIF DM 561 228 PolC1 Staphylococcus epidermidis RP62A GSLPDLPDKA QLSIFDM 562 102 PolC1 Bacillus anthracis Ames GCLGDLPDQN QLSLF 563 946 PolC1Listeria innocua Clip11262 GCLEGLPDQN QLSLF 564 947 PolC1 Listeriamonocytogenes 4b GCLEGLPDQN QLSLF 565 948 PolC1 Listeria monocytogenesEGD-e GCLEGLPDQN QLSLF 566 106 PolC1 Enterococcus faecalis V583GVLKDLPDEN QLSLF DML 567 632 PolC1 Enterococcus faecium DOE GVLKDLPDENQLSLF 568 112 PolC1 Lactococcus lactis IL1403 GVLEGMPDDN QLSLF DDFF 569108 PolC1 Streptococcus equi Sanger GILGNMPDDN QLSLF DDFF 570 107 PolC1Streptococcus pyogenes M1_GAS GILGNMPEDN QLSLF DDFF 571 110 PolC1Streptococcus mutans UA159 GILGSMPEDN QLSLF DDFF 572 111 PolC1Streptococcus thermophilus GILGNMPEDN QLSLF DDFF 573 109 PolC1Streptococcus pneumoniae type_4 GILGNMPEDN QLSLF DELF 574 113 PolC1Ureaplasma urealyticum Serovar_3 GVLDHLSETE QLTLF 575 119 PolC1Mycoplasma genitalium G-37 QLFDEFEHQD DHKLF N 576 120 PolC1 Mycoplasmapneumoniae M129 LLDEFREQDN QKKLF 577 114 PolC1 Mycoplasma pulmonisGIFEQIPETN QIFLI 578 121 PolC1 Clostridium acetobutylicum GCLKGLPESDQLSFF DAI ATCC824D

[0158] TABLE 2 PolB2 Protein Family Sequences Seq. ID Sequence No.Sequence name N-term Motif C-term 405 125 PolB2 Chlorobium tepidum TLSKPQDFSSIFS ADTLF AFSPEGIKVI 406 414 PolB2 Anabaena sp. PCC7120APTTLESNKR QLSLF 407 412 PolB2 Burkholderia cepacia LB400 RDDFTALMSGQKPLF 408 952 PolB2 Ralstonia metallidurans CH34 DDDFETLLTG QMTLF PQ 409200 PolB2 Pseudomonas aeruginosa PAO1 GDDFATLVDR QMALF 410 201 PolB2Pseudomonas putida KT2440 GDDFARLTDH QLLLF 411 226 PolB2 Pseudomonassyringae DC3000 DDDFSTLIGG QLGLF 412 411 PolB2 Pseudomonas fluorescensPf0-1 DDDFSTLIGG QLGLF 413 202 PolB2 Shewanella putrefaciens MR-1KLNYTNIASK QLSLI 414 199 PolB2 Vibrio cholerae N16961 GKQFDELIAP QLGLF415 126 PolB2 Escherichia coli MG1655 EDNFATLMTG QLGLF 416 783 PolB2Salmonella typhi CT18 EDNFATLLTG QLGLF 417 127 PolB2 Salmonellatyphimurium LT2 EDNFATVLTG QLGLF 418 128 PolB2 Klebsiella pneumoniaeMGH78578 NDNFATIVTG QLGLF 419 198 PolB2 Yersinia pestis CO-92 QDDFTTLITGQMGLF 420 124 PolB2 Geobacter sulfurreducens TIGR MKKFAPFLPR ERTLF D

[0159] TABLE 3 DnaE1 Protein Family Sequences Seq. ID Sequence No.Sequence name N-term Motif C-term 421 422 DnaE1 Magnetococcus sp. MC-1TQHQKDQKLG FMNLF GDEEAENSES 422 197 DnaE1 Aquifex aeolicus VF5ANSEKALMAT QNSLF GAPKEEVEEL 423 196 DnaE1 Thermotoga maritima MSB8NKRVEKDILE IRSLF GEKVEQESSN 424 634 DnaE1 Chloroflexus aurantiacusJ-10-fl IEAQKAREIG QSSLF DIFGEATTAN 425 195 DnaE1 Thermus aquaticusAETRERGRSG LVGLF AEVEEPPLVE 426 194 DnaE1 Deinococcus radiodurans R1AEINARAQSG MSMMF GMEEVKKERP 427 193 DnaE1 Porphyromonas gingivalis W83SVVQEEKHSQ SNSLF GEEEDLMIPR 428 674 DnaE1 Bacteroides fragilis NCTC9343NRYQADKAAA VNSLF GGDNVIDIAT 429 421 DnaE1 Cytophaga hutchinsonii JGINAFQTEDDSN QSSLF GDSSSAKPAP 430 192 DnaE1 Chlorobium tepidum TLSQIQNKAVTLG QGGFF NDDFSDGQAG 431 191 DnaE1 Chlamydia trachomatisSREKKEAATG VLTFF SLDSMARDPV 432 190 DnaE1 Chlamydophila pneumoniaeAKDKKEAASG VMTFF TLGAMDRKNE 433 189 DnaE1 Nostoc punctiforme ATCC29133QSRAKDRASG QGNLF DLLGDGFSST 434 1815 DnaE1 Anabaena sp. PCC7120QSRARDRASG QGNLF DLLGGYSSTN 435 188 DnaE1 Synechocystia sp. PCC6803QKRAKEKETG QLNIF DSLTAGESIK 436 187 DnaE1 Prochlorococcus marinus MED4SSRNRDRISG QGNIJF DSISKNDTKE 437 972 DnaE1 Prochlorococcus marinusMIT9313 ASRARDRLSG QGNLF DLVAGAADEQ 438 934 DnaE1 Synechococcus sp.WH8102 SSRAKDRDSG QGNLF DLMAAPNDED 439 186 DnaE1 Treponema denticolaTIGR SQKKENESTG QGSLF EGSGIKEFSD 440 185 DnaE1 Treponema pallidumNichols ARKKAVTSSR QASLF DETDLGECSE 441 184 DnaE1 Borrelia burgdorferiB31 SEDKNNKKLG QNSLF GALESQDPIQ 442 423 DnaE1 Magnetospirillummagnetotacticum AQAAEDRQSS QMSLL GGSNAPTLKL MS-1 443 155 DnaE1Rhodopseudomonas palustris CGA009 QRNHEAATSG QNDMF GGLSDAPSII 444 776DnaE1 Mesorhizobium loti MAFF303099 SLAQQNAVSG QADIF GASLGAQSQA 445 639DnaE1 Brucella suis 1330 QRTQENAVSG QSDIF GLSGAPRETL 446 971 DnaE1Sinorhizobium meliloti 1021 QRAQENKVSG QSDMF GAGAATGPEK 447 933 DnaE1Agrobacterium tumefaciens C58 QMAQNNRTIG QSDMF GSGGGTGPEK 448 157 DnaE1Caulobacter crescentus TIGR QSCHADRQGG QGGLP GSDPGAGRPR 449 156 DnaE1Rhodobacter sphaeroides 2.4.1 AAIHEALNSS QVSLF GEAGADIPEP 450 158 DnaE1Rhodobacter capsulatus SB1003 AAVAEAKSSA QVSLF GEAGDDLPPR 451 935 DnaE1Rickettsia conorii Malish_7 TAYHEEQESN QFSLI KVSSLSPTIL 452 161 DnaE1Rickettsia helvetica TSYHEEQESN QLSLI KVSSLSPTIL 453 159 DnaE1Rickettsia prowazekii Madrid_E TSYHQEQESN QFSLI KVSSLSPTIL 454 160 DnaE1Rickettaia rickettsii TAYHEEQESN QFSLI KVSSLSPTIL 455 681 DnaE1 Cowdriaruminantium SANGER EYNKYNSSFN QISLF NDKNHYKLVE 456 970 DnaE1 Wolbachiasp. TIGR NKNKQDKESS QAALF GSLDVLKPKL 457 635 DnaE1 Sphingomonasaromaticivorans EEASRSRTSG QGGLF GGDDHATPAT SMCC_F199 458 151 DnaE1Neisseria gonorrhoeae FA1090 NADQKAANAN QGGLF DMMEDAIEPV 459 150 DnaE1Neisseria meningitidis Z2491 NADQKAANAN QGGLF DMMEDAIEPV 460 154 DnaE1Nitrosomonas europaea YAEQCSLAAS QVSLF DENTDLIQPP Schmidt_Stan_Watson461 152 DnaE1 Bordetella bronchiseptica RB50 AAEQAARSAN QSSLF GDDSGDVVAG462 153 DnaE1 Bordetella pertussis Tohama_I AAEQAARSAN QSSLF GDDSGDVVAG463 677 DnaE1 Burkholderia pseudomallei K96243 AAEQAAANAL QAGLFDIGGVPAHQH 464 416 DnaE1 Burkholderia cepacia LB400 AAEQASANAL QAGLFDMGDAPSQGH 465 638 DnaE1 Burkholderia mallei ATCC23344 AAEQAAANAL QAGLFDIGGVPAHQH 466 424 DnaE1 Ralstonia metallidurans CH34 LDRTEGESAN QVSLFDLMDDAGASH 467 148 DnaE1 Acidothiobacillus ferrooxidans AQFQSSQASL QESLFSGQEALRVAP ATCC23270 468 149 DnaE1 Xylella fastidiosa EQMSRERESG QNPLFGNADPSTPAI 8.1.b_clone_9.a.5.c 469 420 DnaE1 Xylella fastidiosa Ann-1EQMSRERESG QNSLF GNADPGTPAI 470 419 DnaE1 Xylella fastidiosa DixonEQMSRERESG QNSLF GNADPGTPAI 471 147 DnaE1 Legionella pneumophilaEKEHQNQSSG QFDLF SLLEDKADEQ Philadelphia-1 472 641 DnaE1 Coxiellaburnetii EQRNRDMILG QHDLF GEEVKGIDED Nine_Mile_(RSA_493) 473 640 DnaE1Methylococcus capsulatus TIGR EQQGAMSAAG QDDLF GGFTAESPAA 474 143 DnaE1Pseudomonas aeruginosa PAO1 EQTARSHDSG HMDLF GGVFAEPEAD 475 145 DnaE1Pseudomonas putida KT2440 EQAAHTADSG HVDLF GSMFDAADVD 476 231 DnaE1Pseudomonas syringae DC3000 EQTARSHDSG HSDLF GGLFVEADAD 477 144 DnaE1Pseudomonas fluorescens Pf0-1 EQTARTRDSG HADLF GGLFVEEDAD 478 142 DnaE1Shewanella putrefaciens MR-1 DQHAKAEAIG QHDMF GLLNSDPEDS 479 141 DnaE1Vibrio cholerae N16961 SQHHQAEAFG QADMF GVLTDAPEEV 480 139 DnaE1Pasteurella multocida Pm70 DQHAKDAAMG QADMF GVLTESHEDV 481 137 DnaE1Haemophilus influenzae KW20 DQHAKDEAMG QTDMF GVLTETHEDV 482 138 DnaE1Haemophilus ducreyi 35000HP DQHSKMEALG QSDMF GVLTETPEQV 483 140 DnaE1Actinobacillus DQHAKDEALG QVDMF GVLTETNEEV actinomycetemcomitans HK1651484 230 DnaE1 Buchnera sp. APS KESFRIKSFK QDSLF GIFQNELNQV 485 134 DnaE1Escherichia coli MG1655 DQHAKAEAIG QADMF GVLAEEPEQI 486 784 DnaE1Salmonella typhi CT18 DQHAKAEAIG QTDMF GVLAEEPEQI 487 135 DnaE1Salmonella typhimurium DQHAKAEAIG QTDMF GVLAEEPEQI 488 136 DnaE1Yersinia pestis CO-92 DQHAKAEAIG QVDMF GVLADAPEQV 489 162 DnaE1Desulfovibrio vulgaris QKKLKERDSN QVSLF TMIKEEPKVC Hildenborough 490 164DnaE1 Geobacter sulfurreducens TIGR QKIQQEKESA QVSLF GAEEIVRTNG 491 165DnaE1 Helicobacter pylori KDKANEMMQG GNSLF GAMEGGIKEQ 492 163 DnaE1Campylobacter jejuni NCTC11168 RKMAEVRKNA ASSLF GEEELTSGVQ 493 166 DnaE1Streptomyces coelicolor A3 (2) VAVKRKEAEG QFDLF GGMGDEQSDE 494 167 DnaE1Saccharopolyspora erythraea IGLKRQQALG QFDLF GGGDDAGGEE 495 425 DnaE1Thermobifida fusca YX LSSKKQEAHG QFDLF GGGDEEDGGE 496 170 DnaE1Mycobacterium avium 104 LGTKKAEAMG QFDLF GGDGGCTESV 497 169 DnaE1Mycobacterium leprae TN LGTKKAEAIG QFDLF GGTDGTDAVF 498 973 DnaE1Mycobactenium smegmatis MC2_155 LGTKKAEAMG QFDLF GGGEDTGTDA 499 168DnaE1 Mycobacterium tuberculosis H37RV LGTKKAEALG QFDLF GSNDDGTGTA 500682 DnaE1 Corynebacterium diptheriae TSTKKAADKG QFDLF AGLGADAEEVNCTC13129 501 172 DnaE1 Dehalococcoides ethenogenes TIGR QREQKLKDSNQTTMF DLFGQQSPMP 502 171 DnaE1 Clostridium difficile 630 SMDRKKNVQGQISLF DAFGDSEEDS 503 235 DnaE1 Carboxydothermus hydrogenoformansEFYSKKSNGV QLTLG DFLPEADRYN TIGR 504 233 DnaE1 Bacillus halodurans C-125AEQVKEFQEN TGGLF QLSVEEPEYI 505 785 DnaE1 Bacillus stearothermophilus 10IAIEHAQWVQ ALEAG GLSLKPKYAA 506 173 DnaEl Bacillus subtilis 168HAELFAADDD QMGLF LDESFSIKPK 507 174 DnaE1 Staphylococcus aureus COLVLDGDLNIEQ DGFLF DILTPKQMYE 508 234 DnaE1 Staphylococcus epidermidisRP62A VLDLNSDVEQ DEMLF DLLTPKQSYE 509 175 DnaE1 Bacillus anthracis AmesLKGALEYANL ARDLG DAVPKSKYVQ 510 937 DnaE1 Listeria innocua Clip11262YISLLGEDSK GMNLF AEDDDFLKKM 511 936 DnaE1 Listeria monocytogenes 4bYISLLGEDSK GMNLF AEDDDFLKKM 512 939 DnaE1 Listeria monocytogenes EGD-eYISLLGEDSK GMNLF AEDDEFLKKM 513 176 DnaE1 Enterococcus faecalis V583NIQSILLSGG SMDLL ETLPKEEEIA 514 177 DnaE1 Enterococcus faecium DOEKIQNIVYSGG SLDLL GIMALKEEEV 515 631 DnaE1 Lactococcus lactis IL1403ADHANLLNYY SDDIF MASSGGGFAY 516 976 DnaE1 Streptococcus equi SangerLEGLLTFVNE LGSLF ADSSFSWVET 517 179 DnaE1 Streptococcus pyogenes M1_GASLDGLLVFVNE LGSLF SDSSFSWVDT 516 975 DnaE1 Streptococcus mutans UA159LEHLFTFVNE LGSLF ADSSYNWIEA 519 178 DnaE1 Streptococcus pneumoniaetype_4 LANLFEFVKE LGSLF GDAIYSWQES 520 180 DnaE1 Ureaplasma urealyticumSerovar_3 EKTGLNGHFF DLNLV GLDYAKDMSV 521 182 DnaE1 Mycoplasmagenitalium G-37 NDAKDFWIKS DHLLF TRMPLEKKDS 522 181 DnaE1 Mycoplasmapneumoniae M129 NLAKSFWVQS NHELF PKIPLDQPPV 523 945 DnaE1 Mycoplasmapulmonis LAKVQGDDID ISNFF QLEFSKNSSR 524 183 DnaE1 Clostridiumacetobutylicum SGQRKKNLKG QMNLF TDFVQDDYEE ATCC824D

[0160] TABLE 4 DnaE2 Protein Family Sequences Seq. ID Sequence No.Sequence name N-term Motif C-term 525 664 DnaE2 Rhodopseudomonaspalustris CGAOO9 WAVRRLPDDV PLPLF EAASAREQED 526 771 DnaE2 Mesorhizobiumloti MAFF303099 RALGAKSAAE KLPLF DQPALRLREL 527 667 DnaE2 Brucella suis1330 WAVRRLPNDE TLPLP RAAAASELAQ 528 944 DnaE2 Sinorhizobium meliloti1021 KALDEQSAVE RLPLF EGAGSDDLQI 529 943 DnaE2 Sinorhizobium meliloti1021 LWAIKALRDE PLPLF TAAADREARA 530 940 DnaE2 Agrobacterium tumefaciensC58 LWAIKALRDE PLPLF AAAAIRENAV 531 941 DnaE2 Agrobacterium tumefaciensC58 LWAIKALRDE PLPLF AAAABREATA 532 942 DnaE2 Agrobacterium tumefaciensC58 LWAIKALRDE PLPLF AAAAEREMAA 533 665 DnaE2 Caulobacter crescentusTIGR GLKGEHKAPV QAPLL AGLPLFEERV 534 668 DnaE2 Rhodobacter capsulatusSB1003 WAVRAIRAPK PLPLF ANPLDGEGGI 535 666 DnaE2 Sphingomonasaromaticivoraris LWDVRRTPPT QLPLF AFANAPELGQ SMCC_F199 536 684 DnaE2Bordetella bronchiseptica RES0  AWQAAASAQ SRDLL REAVIVETET 537 683 DnaE2Bordetella parapertussis 12822 ASWQAAASAQ SRDLL REAVIVETET 538 662 DnaE2Bordetella pertussis Tohama_I ASWQAAASAQ SRDLL REAVIVETET 539 678 DnaE2Burkholderia pseudomallei K96243 ALWQAVAAAP ERGLL AAAPIDEAVR 540 656DnaE2 Burkholderia cepacia LB400 RWWAVTAQHA VPRLL RDAPIAEAAL 541 657DnaE2 Ralstonia metallidurans CH34 HARGAAVQTQ HRDLL HDAPPQEHAL 542 661DnaE2 Acidothiobacillus ferrooxidans RHQALWAVQG SLPLP TALPMPVVPEATCC23270 543 663 DnaE2 Methylococcus capsulatus TIGR AFWEAAGVEA PTPLYAEPQFAEAEP 544 659 DnaE2 Pseudomonas aeruginosa PAO1 ARWAVASVEP QLPLFAEGTAIEEST 545 660 DnaE2 Pseudomonas putida KT2440 ARWQVAAVQP QLPLFADVQALPEEP 546 787 DnaB2 Pseudomonas syringae DC3000 ARWEVAGVEA QRPLFDDVTSEEVQV 547 658 DnaE2 Pseudomonas fluorescens Pf0-1 ARWEVAGVQK QLGLFAGLPSQEEPD 548 671 DnaE2 Mycobacterium avium 104 AGAAATQRPD RLPGVGSSSHIPALP 549 672 DnaE2 Mycobacterium leprae TN        RAN RLPGVGGSSHIPVLP 550 974 DnaE2 Mycobacterium smegmatis MC2_155 AGAAATQRPDRLPGV GSSTHIPPLP 551 670 DnaE2 Mycobacterium tuberculosis H37RvAGAAATGRPD RLPGV GSSSHIPALP 552 673 DnaE2 Corynebacterium diptheriaeAGAAATEKAA MLPGL SMVSAPSLPG NCTC13129

[0161] TABLE 5 DinB1 Protein Family Sequences Seq. ID Sequence No.Sequence name N-term Motif C-term  99 444 DinB1 Magnetococcus sp. MC-1SSQTATTQPQ QLSLF 100 441 DinB1 Cytophaga hutchinsonii JGI KLSNLVHGNYQISLF EDSEKNQNLY 101 294 DinB1 Treponema denticola TIGR MNIESDIPEA QTELFYSEKNVKKRK 102 433 DinB1 Magnetospirillum magnetotacticum TDLCPAEDADPPDLF GPRPA MS-1 103 434 DinB1 Magnetospirillum magnetotacticumLGELSRTERR QLDLL TNDEPVRKRL MS-1 104 266 DinB1 Methylobacteriumextorquens AM1 GDLCGAIHAD RGDLA DQGIERVARR 105 432 DinB1Rhodopseudomonas palustris CGA009 SALTEQTGPA EDDML DRRSAHAERA 106 775DinB1 Mesorhizobium loti MAFF303099 LGDVLPPDQR QLRFEL 107 772 DinB1Mesorhizobium loti MAFF303099 SDLSDDDKAD PPDLV DVQSRKRAMA 108 774 DinB1Mesorhizobium loti MAFF303099 VSHLEESAEL QLDLPL GLADEKRRPG 109 650 DinB1Brucella suis 1330 SDLSPSDRAD PPDLV DIQATKRAVA 110 930 DinB1Sinorhizobium meliloti 1021 SDLVDPDLAD PPDLV DPQASRRAAA 111 242 DinB1Sinorhizobium meliloti 1021 LDTVDDRSEP QLALAL 112 931 DinB1Agrobacterium tumefaciens C58 SDLRDAGLAD PPDLV DRQATRRAAA 113 929 DinB1Agrobacterium tumefaciens C58 DQEAEDEEQP QLDLAL 114 267 DinB1Caulobacter crescentus TIGR LTEFVDADTA GADMF ADEERRALKS 115 435 DinB1Rhodobacter sphaeroides 2.4.1 AGAAEADLTG TGDLL DPNAGRRIAA 116 265 DinB1Rhodobacter capsulatus SB1003 DLSPAGGRDP IGDILL DPQATARAAA 117 643 DinB1Sphingomonas aromaticivorans AEDGPSGAAL QAELPF SMCC_F199 118 263 DinB1Neisseria gonorrhoeae FA1090 GVGRLVPKNQ QQDLW A 119 262 DinB1 Neisseriameningitidis Z2491 GVGHLVPKNQ QQDLW A 120 431 DinB1 Nitrosomonaseuropaea SALLKENYYF QEELF Schmidt_Stan_Watson 121 264 DinB1 Bordetellapertussis Tohama_I FPDAQAEAPR QAELF GDAF 122 680 DinB1 Burkholderiapseudomallei K96243 IDEDTAERHG QIALF 123 430 DinB1 Burkholderia cepaciaLB400 ALTPPRRLPV QADLP FASDE 124 644 DinB1 Burkholderia mallei ATCC23344IDEDTAERHG QIALF DDEDMSDEDA 125 445 DinB1 Ralstonia metallidurans CH34ADQGDDPAPV QEELRF DAEPDSPVFR 126 410 DinB1 Acidothiobacillusferrooxidans NVEAVPPEAL QMNLL EEPVDLR ATCC23270 127 260 DinB1 Legionellapneumophila LKQENTYQSV QLPLL DL Philadelphia-1 128 645 DinB1 Coxiellaburnetii SFSEDPLLEL QRTFEW Nine_Mile_(RSA_493) 129 257 DinB1 Pseudomonasaeruginosa PAO1 RLLDLQGAHE QLRLF 130 258 DinB1 Pseudomonas putida KT2440RLRDLRGAHE QLELF PPK 131 259 DinB1 Pseudomonas syringae DC3000RLHDLRDAHE QLELF ST 132 428 DinB1 Pseudomonas fluorescens Pf0-1RLEDLRGGFE QMELF ER 133 409 DinB1 Shewanella putrefaciens MR-1LISEVDPLQT QLVLSI 134 256 DinB1 Vibrio cholerae N16961 VMLKPELQMK QLSMFPSDGWQ 135 248 DinB1 Pasteurella multocida Pm70 PETTESKTQV QMSLW 136 254DinB1 Haemophilus influenzae KW20 VNLPEENKQE QMSLW 137 255 DinB1Actinobacillus VTLPEEKQSE QMSLW actinomycetemcomitans HK1651 138 237DinB1 Escherichia coli MG1655 VTLLDPQMER QLVLGL 139 238 DinB1 Salmonellatyphi CT18 VTLLDPQLER QLVLGL 140 239 DinB1 Salmonella typhimurium LT2VTLLDPQLER QLVLGL 141 240 DinB1 Klebsiella pneumoniae MGH78578VTLLDPQLER QLLLGI 142 241 DinB1 Yersinia pestis CO-92 VTLLDPQLER QLLLDWG 143 270 DinB1 Desulfovibrio vulgaris LGVSHFGGER QMSLPI GGMPRRDDTRHildenborough 144 268 DinB1 Geobacter sulfurreducens TIGR AISNLVHASEQLPLF PEERRLTTLS 145 269 DinB1 Geobacter sulfurreducens TIGR RITNLCYQREQLPLF EKERRKALAT 146 438 DinB1 Streptomyces coelicolor A3 (2) SLTSAEHASHQLTFDP VDEKVRRIEE 147 446 DinB1 Thermobifida fusca YX GLVSADRVHH QLALDEEGPGWRAVE 148 244 DinB1 Mycobacterium avium 104 VSGIDRDGAQ QLMLPFEGRPPDAIDA 149 272 DinB1 Mycobacterium avium 104 VGFSGLSEVR QESLFPDLEMPAPQS 150 245 DinB1 Mycobacterium smegmatis MC2_155 VSNIDRGGTQQLELPF AEQPDPVAID 151 273 DinB1 Mycobacterium smegmatis MC2_155VGFSGLSDIR QESLF PDLEQPEEFP 152 271 DinB1 Mycobacterium tuberculosisH37Rv VGFSGLSDIR QESLF ADSDLTQETA 153 274 DinB1 Corynebacteriumdiptheriae VGLSGLEDAR QDILF PELDRVVPVK NCTC13129 154 276 DinB1Dehalococcoides ethenogenes TIGR GISDFCGPEK QLEIDP ARARLEKLDA 155 443DinB1 Desulfitobacterium hafniense DCB-2 TASRLQKGIE QLSLF QEESEEQTEL 156275 DinB1 Clostridium difficile 630 NLSDKKETYK DITLF EYMDSIQM 157 293DinB1 Carboxydothermus hydrogenoformans TPLVPVGGGR QISLF GEDLRRENLY TIGR158 285 DinB1 Bacillus halodurans C-125 DVIDKKYAYE PLDLP RYEEQIKQAT 159283 DinB1 Bacillus stearothermophilus 10 HVFDEREEGK QLDLF RYEEEAKVEE 160282 DinB1 Bacillus subtilis 168 DLVEKEQAYK QLDLF SFNEDAKDEP 161 286DinB1 Staphylococcus aureus COL VGNLEQSTYK NMTIY DFI 162 287 DinB1Staphylococcus epidermidis RP62A VGSLEQSDFK NLTIY DFI 163 284 DinB1Bacillus anthracis Ames EIEWKTESVK QLDLF SFEEDAKEEP 164 980 DinB1Listeria innocua Clip11262 VTNLKPVYFE NLRLE GL 165 977 DinB1 Listeriamonocytogenes 4b VTNLKPVYFE NLRLE GL 166 978 DinB1 Listeriamonocytogenes EGD-e VTNLKPVYFE NLRLE GL 167 288 DinB1 Enterococcusfaecalis V583 NLDPLAYENI VLPLW EKS 168 439 DinB1 Enterococcus faeciumDOE NLDPMTYENI VLPLW ENQEI 169 779 DinB1 Lactococcus lactis IL1403GVTVTEFGAQ KATLDM Q 170 932 DinB1 Streptococcus equi Sanger TMTGLKDKVTDILLD LSFN 171 247 DinB1 Streptococcus pyogenes M1_GAS TMTMLEDKVA DISLDL172 440 DinB1 Streptococcus mutans UA159 VTALEDSTRE ELSLT ADDFKT 173 289DinB1 Ureaplasma urealyticum Serovar_3 KLVKKENVKK QLFLF D 174 291 DinB1Mycoplasma genitalium G-37 LKKIDTDEGQ KKSLF YQFIPKSISK 175 290 DinB1Mycoplasma pneumoniae M129 LKNNPSSSRP EGLLF YEYQQAKPKQ 176 984 DinB1Mycoplasma pulmonis DFGDIYQSDL SFDLF DQKYDSKKEK 177 292 DinB1Clostridium acetobutylicum LSGLCSGSSV QISMF DEKTDTRNEI ATCC824D

[0162] TABLE 6 DinB2 Protein Family Members Seq. ID Sequence No.Sequence name N-term Motif C-term 178 987 DinB2 Fibrobacter succinogenesTIGR ANNVLEATQE SYDLF TDVKKIEREK 179 279 DinB2 Bacillus halodurans C-125LSNLTSDEAW QLSFF GNRDRAHQLG 180 398 DinB2 Bacillus subtilis LSNIEDDVNQQLSLF EVDNEKRRKL 181 277 DinB2 Bacillus subtilis 168 LSQLSSDDIW QLNLFQDYAKKMSLG 182 280 DinB2 Staphylococcus aureus COL LSQFINEDER QLSLFEDEYQRKRDE 183 281 DinB2 Staphylococcus epidermidis RP62A LTQFIKESDRQLNLF IDEYERKKDV 184 399 DinB2 Bacillus anthracis LTNLLQEGEE QISLFDNVTQREQEV 185 278 DinB2 Bacillus anthracis Ames LTKLIGEGEE QISLFDNIIQREKEI 186 981 DinB2 Listeria innocua Clip11262 CGKLTLKTGL QLNLFEDATRTLNHE 187 983 DinB2 Listeria innocua Clip11262 CAGIKRKTSM QLSVFEDYTKTLQQE 188 985 DinB2 Listeria monocytogenes 4b CGKITLKTGL QLNLFEDATRTLNHE 189 979 DinB2 Listeria monocytogenes EGD-e CGKITLKTGL QLNLFEDFTQTLNHE 190 401 DinB2 Enterococcus faecalis YGRLVWNKNL QLDLFPVPEEQIHET 191 998 DinB2 Enterococcus faecalis V583 YGKLVWNESL QLDLFSEPEEQISEM 192 997 DinB2 Enterococcus faecalis V583 FGKLVWDTTL QIDLFSPPEEQIINN 193 995 DinB2 Enterococcus faecium DOE CSDLVYATGL QLNLFEDPEKQINEA 194 996 DinB2 Enterococcus faecium DOE CSKLVYSNAL QLDLFEDPNEQVKDL 195 403 DinB2 Lactococcus lactis DCP3147 GNQLSDSSVK QLSLFESVQENQTNK 196 402 DinB2 Lactococcus lactis DRC3 ANNLIDEPYQ LISLFDSDEENEETI 197 999 DinB2 Streptococcus gordonii YSDFVDQEYG LISLFDDPLQVQKEE 198 986 DinB2 Streptococcus gordonii GNQLSDSSVK QLSLFESVQENQTNK 199 404 DinB2 Streptococcus pneumoniae SP1000 YSGLVDESFGLISLF DDIEKIEKEE

[0163] TABLE 7 UmuC Protein Family Members Seq. ID Sequence No. Sequencename N-term Motif C-term 229 450 UmuC Magnetococcus sp. MC-1 LLFLVSAQHFQPSLF APPPRLPNSR 230 316 UmuC Porphyromonas gingivalis W83 ILSDLVAEAYQLNLF DPIDRMRQER 231 675 UmuC Bacteroides fragilis NCTC9343 VIITEITDSTQLGLF DSVDREKRKR 232 451 UmuC Cytophaga hutchinsonii JGI VSGIVPEDRVQQNLF DTVDRSKHNK 233 452 UmuC Cytophaga hutchinsonii JGI VIDIVPEEKIQLNLF EPQKNARLHA 234 449 UmuC Prochlorococcus marinus MED4 MQDLTNCKYLQQSII NYESQEESKK 235 781 UmuC Prochlorococcus marinus MIT9313 MQNLQSADHLQQHLL VAVHADEQHR 236 448 UmuC Synechococcus sp. WH8102 MQHLQGTELL QSHLLVPLSEAQQQR 237 447 UmuC Methylobacterium extorquens AM1 STDLVPLEAS QRALIGAFDRERGGA 238 261 UmuC Acidothiobacillus ferrooxidans LLEITSADAL QADLFLSAEEEARAH ATCC23270 239 453 UmuC Legionella pneumophila LEDLIPKKPRQLDMF HQPSDEHLKH Philadelphia-1 240 454 UmuC Legionella pneumophilaLGDLIEKNCL QLDLF NQVSEKELNQ Philadelphia-1 241 317 UmuC Pseudomonassyringae A2 LMDICQPGEF TDDLF TIDQPASADR 242 951 UmuC Shewanellaputrefaciens 5/9/101 LGDFYAPGVF QLGLF DEAKPQPKSK 243 314 UmuC Shewanellaputrefaciens MR-1 LIELMPTKHI QYDLF HAPTENPALM 244 307 UmuC Morganellamorganii MLSDLQGYET QLDLF SPAAVRPGSE 245 309 UmuC Providencia rettgeriLSDFYDPGMF QPGLF DDVSTRSNSQ 246 305 UmuC Escherichia coli MLADFSGKEAQLDLF DSATPSAGSE 247 295 UmuC Escherichia coli MG1655 LGDFFSQGVA QLNLFDDNAPRPGSE 248 304 UmuC Shigella flexneri SA100 LADFTPSGIA QPGLFDEIQPRKNSE 249 310 UmuC Salmonella typhi CT18 MLSSMTDGTE QLSLFDERPARRGSE 250 301 UmuC Salmonella typhi CT18 LNDFTPTGIS QLNLFDEVQPHERSE 251 296 UmuC Salmonella typhi CT18 LGGFFSQGVA QLNLFDDNAPRAGSA 252 303 UmuC Salmonella typhimurium LADFTPSGIA QPGLFDEIQPRKNSE 253 306 UmuC Salmonella typhimurium MLADFSGKEA QLDLFDSATPSAGSE 254 302 UmuC Salmonella typhimurium LNDFTPTGVS QLNLFDEVQPRERSE 255 297 UmuC Salmonella typhimurium LGDFFSQGVA QLNLFDDNAPRAGSA 256 313 UmuC Klebsiella pneumoniae MGH78578 LNDFTGSGVS QLQLFDERPPRPHSA 257 298 UmuC Klebsiella pneumoniae MGH78578 LGDFYSQGVA QLNLFDDNAPRKGSE 258 299 UmuC Klebsiella pneumoniae MGH78578 LGDFYSQGVA QLNLFDELAPRHNSA 259 308 UmuC Serratia marcescens MLSDLQGHET QLDLF APAAVRPGSE260 315 UmuC Desulfovibria vulgaris LFGLEPAAGR QGSLL DLLDGSHEHKHildenborough

[0164] TABLE 8 MutS1 Protein Family Sequences Seq. ID Sequence No.Sequence name N-term Motif C-term 324 493 MutS1 Magnetococcus sp. MC-1QGHAPASQPY QLTLF EDAPPSPALL 325 321 MutS1 Aquifex aeolicus VF5RELEEKENKK EDIVP IJIJEETFKKSE 326 322 MutS1 Aquifex pyrophilusLKELEGEKGK QEVLP FLEETYKKSV 327 365 MutS1 Thermotoga maritima MSB8KNGKSNRFSQ QIPLF PV 328 964 MutS1 Chloroflexus aurantiacus J-10-flVPAQETGQGM QLSFF DLAPHPVVEY 329 364 MutS1 Porphyromonas gingivalis W83DEKGRSIDGY QLSFF QLDDPVLSQI 330 676 MutS1 Bacteroides fragilis NCTC9343AEVSENRGGM QLSFF QLDDPILCQI 331 473 MutS1 Cytophaga hutchinsonii JGIKLKEVPKSTL QMSLF EAADPAWDSI 332 363 MutS1 Chlorobium tepidum TLSQALPLRVESR QISLF EEEESRLRKA 333 361 MutS1 Chlamydia trachomatisD/UW-3/CX DLRPEPEKAQ QLVMF 334 362 MutS1 Chlamydophila pneumoniaeITRPAQDKMQ QLTLF 335 360 MutS1 Synechocystis sp. PCC6803 AAEAAEDQAKQLDIF GF 336 963 MutS1 Fibrobacter succinogenes TIGR AQNKKIKAQP QMDLFAPPDENTLLL 337 359 MutS1 Treponema denticola TIGR EKTPSSPAEK GLSLFPEEELILNEI 338 358 MutS1 Treponema pallidum Nichols AASKPCAQRV SADLFTQEELIGAEI 339 357 MutS1 Borrelia burgdorferi B31 VGREGNSCLE FLPHVSSDGNDKEIL 340 474 MutS1 Magnetospirillum magnetotacticum QASGMARLADDLPLF AALAKPVAAS MS-1 341 475 MutS1 Magnetospirillum magnetotacticumRERPTRRRIE DLPLF ASLAAAPPPP MS-1 342 476 MutS1 Rhodopseudomonaspalustris CGA009 DRGQPKTLID DLPLF AITARAPAEA 343 777 MutS1 Mesorhizobiumloti MAFF303099 VSGKTNRLVD DLPLF SVAMKREAPK 344 962 MutS1 Brucella suis1330 TSGKADRLID DLPLF SVMLQQEKPK 345 343 MutS1 Sinorhizobium meliloti1021 RKNPASQLID DLPLF QVAVRREEAA 346 953 MutS1 Agrobacterium tumefaciensC58 RKNPASQLID DLPLF QIAVRREETR 347 344 MutS1 Caulobacter crescentusTIGR SKDQSPAKLD DLPLF AVSQAVAVTS 348 477 MutS1 Rhodobacter sphaeroides2.4.1 SGGRRQTLID DLPLF RAAPPPPAPA 349 955 MutS1 Rickettsia conoriiMalish_7 GKNILSTESN NLSLF YLEPNKTTIS 350 342 MutS1 Rickettsia prowazekiiMadrid_E EKNILSNASN NLSLF NFEHEKPISN 351 655 MutS1 Sphingomonasaromaticivorans ATGGLAAGLD DLPLF AAAIEAAEEK SMCC_F199 352 340 MutS1Neisseria gonorrhoeae FA1090 LENQAAANRP QLDIF STMPSEKGDE 353 339 MutS1Neisseria meningitidis Z2491 LENQAAANRP QLDIF STMPSEKGDE 354 478 MutS1Nitrosomonas europaea LEQETLSRSP QQTLF ETVEENAKAV Schmidt_Stan_Watson355 341 MutS1 Bordetella bronchiseptica RB50 RLEAQGAPTP QLGLF AAALDADVQS356 959 MutS1 Bordetella pertussis Tohama_I RLEAQGAPTP QLGLF AAALDADVQS357 958 MutS1 Burkholderia pseudomallei K96243 EQQSAAQATP QLDLFAAPPVVDEPE 358 480 MutS1 Burkholderia cepacia LB400 EQQSAAQPAP QLDLFAAPMPMLLED 359 652 MutS1 Burkholderia mallei ATCC23344 EQQSAAQATP QLDLFAAPPVVDEPE 360 481 MutS1 Ralstonia metallidurans CH34 EQSADATPTP QMDLFSAQSSPSADD 361 337 MutS1 Acidothiobacillus ferrooxidans RSSLSHTAPA QLSLFQAAPHPAVYR ATCC23270 362 338 MutS1 Xylella fastidiosa ITPLALDAPQ QCSLFASAPSAAQEA 8.1.b_clone_9.a.5.c 363 483 MutS1 Xylella fastidiosa Ann-1ITPLALDAPQ QCSLF ASAPSAAQEA 364 482 MutS1 Xylella fastidiosa DixonITPLALDAPQ QCSLF ASAPSAAQEA 365 336 MutS1 Legionella pneumophilaQIQDTQSILV QTQII KPPTSPVLTE Philadelphia-1 366 654 MutS1 Coxiellaburnetii PVISETQQPQ QNELF LPIENPVLTQ Nine_Mile_(RSA_493) 367 651 MutS1Methylococcus capsulatus TIGR SAHQQAAPVA QLDLF LPPVVDEPEC 368 331 MutS1Pseudomonas aeruginosa PAO1 QQSGKPASPM QSDLF ASLPHPVIDE 369 332 MutS1Azotobacter vinelandii OP REAGKPQPPI QSDLF ASLPHPLMEE 370 333 MutS1Pseudomonas putida KT2440 KAKDAPQVPH QSDLF ASLPHPAIEK 371 957 MutS1Pseudomonas syringae DC3000 AKPGKPAIPQ QSDMF ASLPHPVLDE 372 484 MutS1Pseudomonas fluorescens Pf0-1 AAKGKPAAPQ QSDMF ASLPHPVLDE 373 319 MutS1Shewanella putrefaciens MR-1 HQVEGTKTPI QTLLA LPEPVENPAV 374 485 MutS1Vibrio parahaemolyticus PRPSTVDVAN QLSLI PEPSEIEQAL 375 326 MutS1 Vibriocholerae N16961 RKPSRVDIAN QLSLI PEPSAVEQAL 376 327 MutS1 Pasteurellamultocida Pm70 DLRQLNQTQG ELALM EEDDSKTAVW 377 328 MutS1 Haemophilusinfluenzae KW20 IQDLRLLNQR QGELF FEQETDALRE 378 329 MutS1 Haemophilusducreyi 35000HP QQTKMAQQHP QADLL FTVEMPEEEK 379 330 MutS1 ActinobacillusIQDLRLLNQR QGELA FESAEDENKD actinomycetemcomitans HK1651 380 323 MutS1Escherichia coli MG1655 NAAATQVDGT QMSLL SVPEETSPAV 381 487 MutS1Salmonella enteritidis LK5 NAAATQVDGT QMSLL AAPEETSPAV 382 486 MutS1Salmonella typhi CT18 NAAATQVDGT AMSLL AAPEETSPAV 383 324 MutS1Salmonella typhimurium NAAATQVDGT QMSLL AAPEETSPAV 384 325 MutS1Yersinia pestis CO-92 NAAASTIDGS QMTLL NEEIPPAVEA 385 488 MutS1 Yersiniapseudotuberculosis NAAASTIDGS QMTLL NEEIPPAVEA IP32953 386 966 MutS1Geobacter sulfurreducens TIGR KRAGAPKPSP QLSLF DQGDDLLRRR 387 489 MutS1Desulfitobacterium hafniense DCB-2 EHLLNKEKAT QLSLF EVQPLDPLLQ 388 490MutS1 Clostridium difficile 630 EDSVKEVALT QISFD SVNRDILSEE 389 356MutS1 Carboxydothermus hydrogenoformans GLKVKDTVPV QLSLF EEKPEPSGVI TIGR390 347 MutS1 Bacillus halodurans C-125 KEVASTNEPT QLSLF EPEPLEAYKP 392491 MutS1 Bacillus stearothermophilus 10 EGVLAEAAFE QLSMF PDLAPAPVEP 392345 MutS1 Bacillus subtilis 168 QKPQVKEEPA QLSFF DEAEKPAETP 393 348MutS1 Staphylococcus aureus COL TLSQKDFEQA SFDLF ENDQKSEIEL 394 349MutS1 Staphylococcus epidermidis RP62A HTSNHNYEQA TFDLF DGYNQQSEVE 395346 MutS1 Bacillus anthracis Ames ETKVDNEEES QLSFF GAEQSSKKQD 396 960MutS1 Listeria innocua Clip11262 KQPEEIHEEV QLSMF PVEPEEKASS 397 961MutS1 Listeria monocytogenes EGD-e KQPEEVHEEV QLSMF PLEPEKKASS 398 350MutS1 Enterococcus faecalis V583 EVSEVHEETE QLSLF KEVSTEELSV 399 492MutS1 Enterococcus faecium DOE IQDRVKEENQ QLSLF SELSENETEV 400 351 MutS1Streptococcus equi Sanger VRETQQLANQ QLSLF TDDGSSSEII 401 352 MutS1Streptococcus pyogenes M1_GAS VESSSAVRQG QLSLF GDEEKAHEIR 402 353 MutS1Streptococcus mutans UA159 ETKESQPVEE QLSLF AIDNNYEELI 403 354 MutS1Streptococcus pneumoniae type_4 PMRQTSAVTE QISLF DRAEEHPILA 404 320MutS1 Clostridium acetobutylicum VKEEPKKDSY QIDFN YLERESILKE ATCC824D

[0165] TABLE 9 RepA Protein Family Sequences Seq. ID Sequence No.Sequence name N-term Motif C-term 579 1002 RepA Acidothiobacillusferrooxidans PVSDTAFAGW QLSLF QGFLANTDDQ 580 1001 RepA Buchneraaphidicola  MLLF KILQSKFKKD 581 1000 RepA Escherichia coli EKLDVIKDSPQMSLF EIIESPAKKD

[0166] TABLE 10 DinB3 Protein Family Sequences Seq. ID Sequence No.Sequence name N-term Motif C-term 200 993 DinB3 Magnetospirillummagnetotacticum AEEVVPAGAE QPRLW GASSGEDARA MS-1 201 467 DinB3Methylobacterium extorquens AM1 ASRVEPLAER QNSHL AAGQQAPDLA 202 464DinB3 Rhodopseudomonas palustris CGA009 ASVSVAVTEA QRGFD TTAHQAEDVA 203773 DinB3 Mesorhizobium loti MAFF303099 VLAAAAFDMA QADLT GEVTDDGADI 204648 DinB3 Brucella suis 1330 ALRSSTVAQR QTGLD QHEEDEAGFS 205 463 DinB3Sinorhizobium meliloti 1021 VLRSERLDPA QQDFS GAPDESQLLA 206 990 DinB3Agrobacterium tumefaciens C58 AVMTEPLEEA QKASA LIGDDVTDVT 207 988 DinB3Agrobacterium tumefaciens C58 ATHAEPLVAA QARSS LLDEGRAEIA 208 989 DinB3Agrobacterium tumefaciens C58 AVMAEPLEER QKSSS LVEDEVTDVT 209 468 DinB3Caulobacter crescentus TIGR AFAVEPMAAA QARLD ADAAASADET 210 465 DinB3Rhodobacter capsulatus SB1003 ATRVEPLAPA QLGTT PAASPDRLAD 211 649 DinB3Sphingomonas aromaticivorans LPVTEPLAAS QPTLD GSGQETTEVA SMCC_F199 212462 DinB3 Bordetella bronchiseptica RB50 APDTVPQPAA STCLF PEPGGTPADH 213991 DinB3 Bordetella parapertussis 12822 APDTVPQPAA STCLF PEPGGTPADH 214679 DinB3 Burkholderia pseudomallei K96243 ATRVESVAPP ADDLF PEPGGTREAR215 459 DinB3 Burkholderia cepacia LB400 ADQVGEYAGQ SDTLF PMPESDGDSI 216646 DinB3 Burkholderia mallei ATCC23344 ATRIESVAPP ADDLF PEPGGTREAR 217460 DinB3 Ralstonia metallidurans CH34 VEAMEICVPQ SDSLF PEPGAEPAEL 218461 DinB3 Acidothiobacillus ferrooxidans ALAPQHWPGR QATWW QDGVEEARWQATCC23270 219 647 DinB3 Methylococcus capsulatus TIGR SADIQPFTLP TADLFTPGAAGGESW 220 455 DinB3 Pseudomonas aeruginosa PAO1 ARELPPFTPQ HRELFDERPQQYLGW 221 456 DinB3 Pseudomonas putida KT2440 AEDLPPFVPQ HRELFDERPQQYLGW 222 457 DinB3 Pseudomonas syringae DC3000 ARDLPDFVPA HRELFDERVQQTLPW 223 458 DinB3 Pseudomonas fluorescens Pf0-1 AEDLPSFVPQ FQELFDDRPQQTLPW 224 992 DinB3 Mycobacterium avium 104 AVEVVSAEAL QLPLW GGLG225 470 DinB3 Mycobacterium smegmatis MC2_155 PVEVVSSAAL QLPLWGGIGEEDRLR 226 469 DinB3 Mycobacterium tuberculosis H37Rv VETVSASEGLQLPLW GGLGEQDRLR 227 471 DinB3 Corynebacterium diptheriae LRPYECMRPSQPQLW GTNKSDEESE NCTC13129 228 994 DinB3 Corynebacterium glutamicumAHP-3 PLECVPPDMA SGGLW DTGRSQQHVA

[0167] TABLE 11 Duf72 Protein Family Sequences Seq. ID Sequence No.Sequence name N-term Motif C-term 300 850 Duf72 Nostoc punctiformeATCC29133 PWNNLEHPPN QLSLW S 301 851 Duf72 Anabaena sp. PCC7120PWNHLDYPPH QLNLW 302 843 Duf72 Pseudomonas aeruginosa PAO1 PEPIPAPEVEQLGLL 303 927 Duf72 Pseudomonas putida KT2440 PELPRAPEVE QLGLL 304 842Duf72 Pseudomonas syringae DC3000 PELDRGPQVE QLGLL 305 928 Duf72Pseudomonas fluorescens Pf0-1 PELYREPAAE QLGLL 306 845 Duf72 Shewanellaputrefaciens MR-1 LDKKPEETST QMGLSW 307 844 Duf72 Vibrio cholerae N16961APFPVTPEQP QLSMF 308 852 Duf72 Pasteurella multocida Pm70 VKPKPEFLTGQQSLF 309 848 Duf72 Escherichia coli MG1655 EIGAVPAIPQ QSSLF 310 847Duf72 Salmonella typhi CT18 EIGTAPSIPQ QSSLF 311 846 Duf72 Salmonellatyphimurium EIGTAPSIPQ QSSLF 312 849 Duf72 Yersinia pestis CO-92TLPTAPDWPE QETLF 313 835 Duf72 Bacillus halodurans C-125 EIEYRGLTPKQLNLF E 314 836 Duf72 Bacillus stearothermophilus 10 GIEYTGLAPR QLGLF315 834 Duf72 Bacillus subtilis 168 DIEYSGLAPR QLDLF 316 839 Duf72Staphylococcus aureus NIEYEGLAPQ QLKLF 317 838 Duf72 Staphylococcusepidermidis RP62A DIDYEGLAPQ QLKLF 318 837 Duf72 Bacillus anthracis AmesNITYGEPKPE QLNLF E 319 833 Duf72 Listeria innocua Clip11262 QVEFQGLAPMQMDLF SE 320 832 Duf72 Listeria monocytogenes QVEFQGLAPM QMDLF SE 321853 Duf72 Pediococcus acidilactici GIHFTGLGPM QLDLF 322 840 Duf72Enterococcus faecalis V583 NLSYDDLNPK QLDLF 323 841 Duf72 Enterocoocusfaecium DOE NIKPDGLNPT QMDLF

[0168] TABLE 12 DnaA2 Protein Family Sequences Seq. ID Sequence No.Sequence name N-term Motif C-term 261 891 DnaA2 Magnetococcus ap. MC-1MHTGSA QLLIAF PLDPVLSWEN 262 892 DnaA2 Magnetospirillum magnetotacticumMSEA QLPLAF GHVPSLAAED MS-1 263 894 DnaA2 Rhodopseudomonas palustrisCGA009 VEPR QLALDL PHAESLSRED 264 895 DnaA2 Mesorhizobium lotiMAFF303099 MTAQRTDPPR QLPLDL GHGTGYSRDE 265 896 DnaA2 Sinorhizobiummeliloti 1021 MKRHLSE QLPLVF GHAPATGRDD 266 893 DnaA2 Agrobacteriumtumefaciens C58 KTDNARSKAE QLPLAF SHQSASGRED 267 897 DnaA2 Caulobactercrescentus TIGR MST QFKLPL ASPLTHGRED 268 899 DnaA2 Rhodobactersphaeroides 2.4.1 VKG QLAFDL PIRPALSRED 269 898 DnaA2 Rhodobactercapsulatus SB1003 MTR QLPLPL PVRVAEGRED 270 1812 DnaA2 Rickettsiaconorii Malish_7 VQ QYIFRF TTSSKYHPDE 271 900 DnaA2 Rickettsiaprowazekii Madrid_E MQ QYIFHF TPSNKYHPDE 272 1813 DnaA2 Wolbachia sp.TIGR RKRLRKRFNV QLNLF NNNQADYSRQ 273 902 DnaA2 Neisseria gonorrhoeaeFA1090 MN QLIFDF AAHDYPSFDK 274 901 DnaA2 Neisseria meningitidis Z2491MN QLIFDF AAHDYPSFDK 275 903 DnaA2 Nitrosomonas europaea MR QQLLDITEIGPPSLDN Schmidt_Stan_Watson 276 904 DnaA2 Bordetella parapertussis12822 MNR QLLLDV LPAPAPTLNN 277 907 DnaA2 Burkholderia fungorum VLRQLTLDL GTPPPSTFDN 278 906 DnaA2 Burkholderia pseudomallei K96243 VTRQLTLDL GTPPPSTFDN 279 905 DnaA2 Burkholderia mallei ATCC23344 VTR QLTLDLGTPPPSTFDN 280 908 DnaA2 Ralstonia metallidurans CH34 MSPRQK QLSLELGSPPPSTFEN 281 909 DnaA2 Acidothiobacillus ferrooxidans MGNR QRILPLGVQAPATLEG ATCC23270 282 910 DnaA2 Xylella fastidiosa MSVS QLPLALRYSSDQRFET 8.1.b_clone_9.a.5.c 283 911 DnaA2 Legionella pneumophila MNKQLALAI KLNDEATLDD Philadelphia-1 284 912 DnaA2 Coxiella burnetii MIDQLPLRV QLREETTFAN Nine_Mile_(RSA_493) 285 913 DnaA2 Methylococcuscapsulatus TIGR MAQ QIPLHF AVDPLQTFEA 286 914 DnaA2 Pseudomonasaeruginosa PAO1 MKPI QLPLSV RLRDDATFAN 287 915 DnaA2 Pseudomonas putidaKT2440 MKPPI QLPLGV RLRDDATFIN 288 916 DnaA2 Pseudomonas syringae DC3000MKPI QLPLSV RLRDDATFVN 289 917 DnaA2 Pseudomonas fluorescens Pf0-1 MKPIQLPLGV RLRDDATFIN 290 919 DnaA2 Shewanella putrefaciens MR-1 DVRVPLNSPLQLSLPV YLPDDETFNS 291 918 DnaA2 Pasteurella multocida Pm70 FVGCFLLENFQLPLPI HQLDDETLDN 292 920 DnaA2 Haemophilus influenzae KW20 MNK QLPLPIHQIDDATLEN 293 921 DnaA2 Haemophilus ducreyi 35000HP NWSIRFKNSL QLLLPIHQIDDETLDS 294 922 DnaA2 Actinobacillus MSEPHF QLPLPI HQLDDDTLENactinomycetemcomitans HK1651 295 923 DnaA2 Escherichia coli MG1655VEVSLNTPA QLSLPL YLPDDETFAS 296 924 DnaA2 Salmonella typhi CT18VEVSLNTPA QLSLPL YLPDDETFAS 297 925 DnaA2 Salmonella typhimuriumVEVSLNTPA QLSLPL YLPDDETFAS 298 926 DnaA2 Yersinia pestis CO-92MVEVLLNTPA QLSLPL YLPDDETFAS 299 1814 DnaA2 Geobacter sulfurreducensTIGR ARSSRPFPAM QLVFDF PVTPKYSFDN

[0169] TABLE 13 Hexapeptide Motif Sequences Seq. ID Sequence No.Sequence name N-term Motif C-term 106 775 DinB1 Mesorhizobium lotiMAFF303099 LGDVLPPDQR QLRFEL 108 774 DinB1 Mesorhizobium loti MAFF303099VSHLEESAEL QLDLPL GLADEKRRPG 111 242 DinB1 Sinorhizobium meliloti 1021LDTVDDRSEP QLALAL 113 929 DinB1 Agrobacterium tumefaciens C58 DQEAEDEEQPQLDLAL 117 643 DinB1 Sphingomonas aromaticivorans AEDGPSGAAL QAELPFSMCC_F199 125 445 DinB1 Ralstonia metallidurans CH34 ADQGDDPAPV QEELRFDAEPDSPVFR 128 645 DinB1 Coxiella burnetii SFSEDPLLEL QRTFEWNine_Mile_(RSA_493) 133 409 DinB1 Shewanella putrefaciens MR-1LISEVDPLQT QLVLSI 138 237 DinB1 Escherichia coli MG1655 VTLLDPQMERQLVLGL 139 238 DinB1 Salmonella typhi CT18 VTLLDPQLER QLVLGL 140 239DinB1 Salmonella typhimurium LT2 VTLLDPQLER QLVLGL 141 240 DinB1Klebsiella pneumoniae MGH78578 VTLLDPQLER QLLLGI 142 241 DinB1 Yersiniapestis CO-92 VTLLDPQLER QLLLDW G 143 270 DinB1 Desulfovibrio vulgarisLGVSHFGGER QMSLPI GGMPRRDDTR Hildenborough 146 438 DinB1 Streptomycescoelicolor A3 (2) SLTSAEHASH QLTFDP VDEKVRRIEE 148 244 DinB1Mycobacterium avium 104 VSGIDRDGAQ QLMLPF EGRPPDAIDA 150 245 DinB1Mycobacterium smegmatis MC2_155 VSNIDRGGTQ QLELPF AEQPDPVAID 154 276DinB1 Dehalococcoides ethenogenes TIGR GISDFCGPEK QLEIDP ARARLEKLDA 169779 DinB1 Lactococcus lactis IL1403 GVTVTEFGAQ KATLDM Q 171 247 DinB1Streptococcus pyogenes M1_GAS TMTMLEDKVA DISLDL 261 891 DnaA2Magnetococcus sp. MC-1 MHTGSA QLLIAF PLDPVLSWEN 262 892 DnaA2Magnetospirillum magnetotacticum MSEA QLPLAF GHVPSLAAED MS-1 263 894DnaA2 Rhodopseudomonas palustris CGA009 VEPR QLALDL PHAESLSRED 264 895DnaA2 Mesorhizobium loti MAFF303099 MTAQRTDPPR QLPLDL GHGTGYSRDE 265 896DnaA2 Sinorhizobium meliloti 1021 MKRHLSE QLPLVF GHAPATGRDD 266 893DnaA2 Agrobacterium tumefaciens C58 KTDNARSKAE QLPLAF SHQSASGRED 267 897DnaA2 Caulobacter crescentus TIGR MST QFKLPL ASPLTHGRED 268 899 DnaA2Rhodobacter sphaeroides 2.4.1 VKG QLAFDL PIRPALSRED 269 898 DnaA2Rhodobacter capsulatus SB1003 MTR QLPLPL PVRVAEGRED 270 1812 DnaA2Rickettsia conorii Malish_7 VQ QYIFRF TTSSKYHPDE 271 900 DnaA2Rickettsia prowazekii Madrid_E MQ QYIFHF TPSNKYHPDE 273 902 DnaA2Neisseria gonorrhoeae FA1090 MN QLIFDF AAHDYPSFDK 274 901 DnaA2Neisseria meningitidis Z2491 MN QLIFDF AAHDYPSFDK 275 903 DnaA2Nitrosomonas europaea MR QQLLDI TEIGPPSLDN Schmidt_Stan_Watson 276 904DnaA2 Bordetella parapertussis 12822 MNR QLLLDV LPAPAPTLNN 277 907 DnaA2Burkholderia fungorum VLR QLTLDL GTPPPSTFDN 278 906 DnaA2 Burkholderiapseudomallei K96243 VTR QLTLDL GTPPPSTFDN 279 905 DnaA2 Burkholderiamallei ATCC23344 VTR QLTLDL GTPPPSTFDN 280 908 DnaA2 Ralstoniametallidurans CH34 MSPRQK QLSLEL GSPPPSTFEN 281 909 DnaA2Acidothiobacillus ferrooxidans MGNR QRILPL GVQAPATLEG ATCC23270 282 910DnaA2 Xylella fastidiosa MSVS QLPLAL RYSSDQRFET 8.1.b_clone_9.a.5.c 283911 DnaA2 Legionella pneumophila MNK QLALAI KLNDEATLDD Philadelphia-1284 912 DnaA2 Coxiella burnetii MID QLPLRV QLREETTFANNine_Mile_(RSA_493) 285 913 DnaA2 Methylococcus capsulatus TIGR MAQQIPLHF AVDPLQTFEA 286 914 DnaA2 Pseudomonas aeruginosa PAO1 MKPI QLPLSVRLRDDATFAN 287 915 DnaA2 Pseudomonas putida KT2440 MKPPI QLPLGVRLRDDATFIN 288 916 DnaA2 Pseudomonas syringae DC3000 MKPI QLPLSVRLRDDATFVN 289 917 DnaA2 Pseudomonas fluorescens Pf0-1 MKPI QLPLGVRLRDDATFIN 290 919 DnaA2 Shewanella putrefaciens MR-1 DVRVPLNSPL QLSLPVYLPDDETFNS 291 918 DnaA2 Pasteurella multocida Pm70 FVGCFLLENF QLPLPIHQLDDETLDN 292 920 DnaA2 Haemophilus influenzae KW20 MNK QLPLPIHQIDDATLEN 293 921 DnaA2 Haemophilus ducreyi 35000HP NWSIRFKNSL QLLLPIHQIDDETLDS 294 922 DnaA2 Actinobacillus MSEPHF QLPLPI HQLDDDTLENactinomycetemcomitans HK1651 295 923 DnaA2 Escherichia coli MG1655VEVSLNTPA QLSLPL YLPDDETFAS 296 924 DnaA2 Salmonella typhi CT18VEVSLNTPA QLSLPL YLPDDETFAS 297 925 DnaA2 Salmonella typhimuriumVEVSLNTPA QLSLPL YLPDDETFAS 298 926 DnaA2 Yersinia pestis CO-92MVEVLLNTPA QLSLPL YLPDDETFAS 299 1814 DnaA2 Geobacter sulfurreducensTIGR ARSSRPFPAM QLVFDF PVTPKYSFDN 306 845 Duf72 Shewanella putrefaciensMR-1 LDKKPEETST QMGLSW

EXAMPLE 2

[0170] In this example, we demonstrate that the peptide motifsidentified in Example 1 are necessary and sufficient to enable thebinding of proteins to β.

A. Methods

[0171] Materials

[0172]E. coli XL-1Blue was used as host for all plasmid constructions.pLexA, pB42AD, p8op-lacZ vectors and yeast EGY48 cells were from theMatchmaker two-hybrid system (Clontech). Minimal synthetic dropout basemedia with 2% glucose (SD) or induction media containing 2% galactoseand 1% raffinose (SG), and different drop out amino acid mixtures (CSM)were obtained from BIO 101. All enzymes used for cloning and PCR werefrom Promega.

[0173] Yeast Two-Hybrid Plasmid Construction

[0174] We used the yeast two-hybrid system based on the LexA DNA bindingdomain and the transactivation domain from the bacterial protein B42.The coding region of E. coli β was amplified by PCR from XL-1 Bluegenomic DNA using Pfu DNA polymerase.

[0175] Oligonucleotide primers forward and reverse primers, respectively5′-TGGCTGGAATTCAAATTTACCGTAGAACGT-3′ (Seq. ID No. 582) and5′-AGTCCAGAATTCTTACAGTCTCATTGGCAT-3′ (Seq. ID No. 583)

[0176] for amplifying the β gene were flanked by EcoRI sites(underlined) that allowed cloning of the β gene in the EcoRI site ofpB42AD creating a translational fusion with the B42 transcriptionalactivation domain. To construct various deletions of the DnaE gene inpLexA, the appropriate portion of the DnaE gene was amplified by PCRusing Pfu DNA polymerase. The PCR primers used to generate DnaE(542-991) and DnaE (736-991) fragments were

[0177] 5′-TTTGATGAATTCAAAAGCGACGTTGAATACGC-3′ (5′ primer starting atamino acid 542, Seq. ID No. 584),

[0178] 5′-GCTTTGGAATTCGTGTCATATCAAACGTTATG-3′ (5′ primer starting atamino acid 736, Seq. ID No. 585), and

[0179] 5′-GACTTTGAATTCTCGAGTTAACCACGTTCTGTCGGGTGCA-3′ (3′ primer, Seq.ID No. 586).

[0180] For construct DnaE (542-735), the primers5′-TTTGATGAATTCAAAAGCGACGTTGAATACGC-3′ (Seq. ID No. 587) and5′-GACTTTGAATTCTCGAGTTACATAACGTTTGATAAGTCAC-3′ (Seq. ID No. 588)

[0181] were used. All forward primers contained EcoRI sites (underlined)and reverse primers were flanked by XhoI sites (underlined) that allowedcloning of each DnaE PCR product into the EcoRI and XhoI sites of pLexA,creating an in frame fusion with the LexA DNA binding domain. For sitedirected mutagenesis, DnaE (736-991) fragment was cloned into pQE11(Qiagen).

[0182] Mutations were introduced in this plasmid using the mutagenicprimers 2HyKK1 with 2HyKK2 for the MF to KK mutation and 2HyPP1 with2HyPP2 for the QF to PP mutation using QuikChange protocol (Stratagene).These primers had the following sequences:5′-GTCAGGCCGATAAAAAGGGCGTGCTGGCC-3′ (2HyKK1,, Seq. ID No. 589)5′-GCCAGCACGCCCTTTTTATCGGCCTGACC-3′ (2HyKK2,, Seq. ID No. 590)5′-GAAGCTATCGGTCCTGCCGATATGCCAGGCGTGCTGGCC-3′ (2HyPP1,, Seq. ID No. 591)and 5′-GGCCAGCACGCCTGGCATATCGGCACCACCGATAGCTTC-3′ (2HyPP2,. Seq. ID No.592)

[0183] PCR fragments containing the mutation were then subcloned intopLexA to generate pLexADnaE (736-991 KK) and pLexADnaE (736-991 PP)plasmids. To subclone peptides containing the β-binding regions, weamplified appropriate regions of DnaE, UmuC, DinB and MutS by PCR usingPfu DNA polymerase. The primers for these amplifications were asfollows: DnaE (908-931) 5′-GGAAAGAATTCGGTCCGGCGGCAGATCAACACGCG-3′(forward,, Seq. ID No. 593) and5′-GATCAACTCGAGAGGACCTCCAGCTCCCGGCTCTTCGGCCAGCAC-3′ (reverse,; Seq. IDNo. 594) DnaE (896-919)5′-TCTCAAAGAATTCGCAGCGGGTGCGAGTCAGGGAGTCGCGCAG-3′ (forward,, Seq. ID No.595) and 5′-AATCCACTCGAGGCCTCCACCGATAGCTTCCGCTTT-3′ (reverse,; Seq. IDNo. 596) UmuC 5′-TCTCAAAGAATTCGCGGGTGCGAGTCAGGGAGTCGCGCAG-3′ (forward,,Seq. ID No. 597) and 5′-AATCCACTCGAGTCCCGGTGCGTTGTCATCGAA-3′ (reverse,;Seq. ID No. 598) DinB 5′-TCTCAAAGAATTCGCGGGTGCGCCGCAAATGGAAAGACAA-3′(forward,, Seq. ID No. 599) and5′-AATCCACTCGAGTCCAGCTCCTAATCCCAGCACCAGTTG-3′ (reverse,; Seq. ID No.600) MutS 5′-TCTCAAAGCCGCCGCTACGCAAGTGG-3′ (forward,, Seq. ID No. 601)and 5′-AATCCACTCGAGTCCAGCTCCTGGTACTGACAGCAAAGAC-3′ (reverse,. Seq. IDNo. 602)

[0184] These PCR fragments were digested with EcoRI and XhoI(underlined) and were fused in frame to LexA binding domain through anGAG or AGA linker. For the construction of pLexAPolB, double strandedDNA encoding the linker GAG and the sequence QLGLF (Seq. ID No. 636)with flanking EcoRI and XhoI sites were subcloned into pLexA.

[0185] The DNA inserts and the cloning junctions in all plasmids wereconfirmed by sequencing.

[0186] Two-Hybrid Assay

[0187] Interaction between β and various LexA-fusion proteins weretested in yeast EGY48 containing a lacZ reporter gene (EGY48p80p-lacZ)by cotransformation of pLexA fusion plasmid and pB42ADβ plasmid usingthe Lithium acetate method. Cotransformants were plated in syntheticcomplete medium lacking appropriate supplements to maintain plasmidselection.

[0188] β-Galactosidase

[0189] Three to six transformants were patched onto indicator medium(SG/Gal/Raf/-His/-Leu/-Trp/-Ura with X-gal), grown at 30° C. and checkedat 12 h intervals up to 96 h for development of blue colour. Resultswere compared with the positive (pLexA-53 with pB42AD-T) and negativecontrols (pLexA-Lam with pB42AD-T) performed in parallel. Cells werealso inoculated and grown to mid-log phase in selective mediumcontaining glucose or galactose. β-Galactosidase activity was estimatedusing Yeast β-Galactosidase kit (Pierce) and enzyme activity expressedin Miller units. All results were reproducible in at least twoindependent assays.

B. Results

[0190] Analysis of the β-Binding Site in E. coli DnaE

[0191] The foregoing bioinformatics analysis in Example 1 allowedidentification of two short conserved peptide motifs in E. coli DnaEthat fulfilled some of the criteria for being part of the β-binding sitein eubacterial proteins. To obtain experimental verification of the roleof the proposed peptide motifs a region of the gene encoding E. coliDnaE flanking the motif was cloned into the yeast two-hybrid vectorpLexA to generate plasmid pLexADnaE (542-991) (FIG. 2). Significantexpression of β-galactosidase was observed in Saccharomyces cerevisiaeEGY48 transformed with plasmids pLexADnaE (542-991) and pB42ADβexpressing E. coli β fused to the transcription activator domain B42(FIG. 2). Removal of the amino-terminal region that did not contain theproposed peptide increased the expression of β-galactosidase in theyeast two-hybrid system. No significant expression of β-galactosidasewas observed from the fragment that did not contain the proposed bindingpeptide. To further characterise the proposed β-binding site,site-directed mutagenesis of the amino acids in the peptide motif wasundertaken to convert the QADMF (Seq. ID No. 631) motif to QADKK (Seq.ID No. 632) (plasmid pLexADnaE (736-991 KK)) and PADMP (Seq. ID No. 633)(plasmid pLexADnaE (736-991 PP)), both predicted to be non-bindingsequences. In S. cerevisiae transformed with plasmids pLexADnaE (736-991KK) or pLexADnaE (736-99 PP1) and pB42ADβ, no significant expression ofβ-galactosidase was observed (FIG. 2). To further examine the role ofthe QADMF (Seq. ID No. 631) peptide a DNA fragment encoding a 24 aminoacid peptide containing the sequence was inserted into the yeasttwo-hybrid vector pLexA to generate plasmid pLexADnaE (908-931),containing an in frame fusion of the peptide with LexA, again strongexpression of β-galactosidase was observed from proteins containing thepeptide and not from cells containing pLexADnaE (896-919) expressingLexA containing the adjacent peptide.

[0192] Analysis of the β-Binding Site in E. coli UmuC

[0193] The foregoing bioinformatics analysis in Example 1 allowedidentification of a short conserved peptide motif in E. coli UmuC thatappeared to fulfil all of the criteria for being part of the β-bindingsite in eubacterial proteins. To obtain experimental verification of therole of the proposed peptide motif a short peptide containing the motif(SQGVAQLNLFDDNAP, Seq. ID No. 637) was expressed as a LexA fusion in theplasmid pLexAUmuC(351-365). Significant expression of β-galactosidasewas observed in S. cerevisiae EGY48 when pLexAUmuC (351-365) plasmidco-transformed with plasmid expressing B42-β fusion (FIG. 2).

[0194] Analysis of the β-Binding Site in E. coli DinB

[0195] The Example 1 analysis also allowed identification of a shortconserved peptide motif in E. coli DinB that represents the hexapeptideβ-binding peptide motif in eubacterial proteins. To obtain experimentalverification of the role of the proposed variant peptide motifPQMERQLVLGL (Seq. ID No. 639), a short peptide containing the motif wasexpressed as a LexA fusion in the yeast two-hybrid vector pLexADinB(FIG. 2). Significant expression of β-galactosidase was observed in S.cerevisiae EGY48 when they were co-transformed with pLexADinB (307-317)plasmid and plasmid expressing B42-β fusion (FIG. 2).

[0196] Analysis of the β-Binding Site in E. coli MutS

[0197] The Example 1 analysis further allowed identification of a shortconserved peptide motif in E. coli MutS that fulfilled all of thecriteria for being part of the β-binding site in eubacterial proteins.To obtain experimental verification of the role of the proposed peptidemotif, a short peptide encoding the motif “AAATQVDGTQMSLLSVP” (Seq. IDNo. 638) was expressed as a LexA fusion in the yeast two-hybrid vectorpLexAMutS(802-818) (FIG. 2). Significant expression of β-galactosidasewas observed in S. cerevisiae EGY48 when they were co-transformed withpLexAMutS (802-818) plasmid and pB42ADβ plasmid FIG. 2). Consistent withthe peptide results, the full-length E. coli MutS protein fused withLexA also interacted with E. coli β in the yeast two hybrid assay.Mutagenesis of LL (in the motif QMSLL: see Seq. ID No. 638) to AA inthis peptide motif eliminated β binding by MutS.

[0198] Analysis of the β-Binding Site in E. coli PolB

[0199] From the Example 1 analysis, a short conserved peptide motif inE. coli PolB was identified that fulfilled all of the criteria for beingpart of the β-binding site in eubacterial proteins. To obtainexperimental verification of the role of the proposed peptide motif ashort peptide encoding the motif “QLGLF” (Seq. ID No. 636) was expressedas a LexA fusion in the yeast two-hybrid vector pLexAPolB(779-783) (FIG.2). Significant expression of β-galactosidase was observed in S.cerevisiae when they were co-transformed with pLexAPolB (779-783)plasmid and pB42ADβ plasmid (FIG. 2).

EXAMPLE 3

[0200] In this example, we describe the identification of a novel δprotein orthologue in Helicobacter pylori.

[0201] Search for Helicobacter pylori δ Orthologue

[0202] The complete amino acid sequence of the identified E. coli andHaemophilus influenzae δ orthologues was used to initiate the followingsearches: BLAST searches of the H. pylori complete genomes sequences,PSI-BLAST searches of the non-redundant database of proteins at the NCBIand BLAST searches of the unfinished and completed genomes at:

[0203] NCBI(http://www.ncbi.nlm.nih.gov/Microb_blast/unfinishedgenome.html),

[0204] TIGR (http://www.tigr.org/cgi-bin/BlastSearch/blast.cgi?),

[0205] Sanger Center(http://www.sanger.ac.uk/DataSearch/omniblast.shtml), and

[0206] DOE Joint Genome Institute(http://spider.jgi-psf.org/JGI_microbial/html/).

[0207] Searches were carried out on a reiterative basis using hits atthe margins of significance to initiate new searches. For the δ proteinthe following criteria were used to determine whether or not to includea particular sequence in the next round of searching: product of similarlength to known holA proteins, identities in similar relative positionsin the proteins, proteins not currently assigned a function. Thisprocess was continued until a candidate putative orthologue of the δprotein had been identified in all bacteria for which a completed orsubstantially completed genome sequence was available. Additionalsearches were also undertaken using the SAM-T98 server athttp://www.cse.ucsc.edu/research/compbio/HMM-apps/T98-query.html.

[0208] Bacterial and Yeast Strains

[0209]E. coli XL-1Blue was used as host for all plasmid constructions.BL21(DE3)pLysS (Novagen) was used for bacterial expression of the His₆tagged proteins. S. cerevisiae strain EGY48 (MATa, his3, trp1, ura3,LexA _(op(X6))-Leu) (Clontech) was used for the two hybrid analyses.Vector pET20b was from Novagen, pLexA and pBD42AD were from Clontech andpESC-LEU from Stratagene.

[0210] Cloning and Expression of Proteins

[0211] To generate various expression plasmids used in the in vitroprotein interaction, the full length genes were amplified by PCR using ahigh fidelity polymerase Pfu DNA Polymerase (Promega). Human PCNA wasamplified from Lambda ZAP colon cancer cDNA library (Stratagene) withthe primers HuPCNA1 and HuPCNA2. The sequences of the foregoing primersand other primers are given in Table 14. In the table, restriction sites(NdeI, NotI, EcoRI and XhoI) are underlined and stop codons doubleunderlined. TABLE 14 Oligonucleotide primers Seq. ID Primer No. SequenceHuPCNA1 603 5′-GGGAATTCCATATGTTCGAGGCGCGCCTGG-3′ HuPCNA2 6045′-CGAAGCTTTGCGGCCGCCAGTCTCATTGGCATGAC-3′ Hpδ1 6055′-GGGAATTCCCATATGTATCGTAAAGATTTG-3′ Hpδ2 6065′-CCGCTCGAGTGCGGCCGCGGGGTTAATGATTTTTTGAAT-3′ Hpδ′1 6075′-GGGAATTCCATATGAAAAACTCCAACCGCCTT-3′ Hpδ′2 6085′-CCGCTCGAGTGCGGCCGCTGGCGTTTTCTTTTTGGATAA-3′ Hpβ1 609 5′-GGGAATTCCATATGGAAATCAGTGTT-3′ Hpβ2 610 5′-CGAAGCTTTGCGGCCGCTTATAGTGTGATTGGCAT-3′ Ecβ1 611 5′-GGCATACATATGAAATTTACCGTAGAA-3′ Ecβ2612 5′-CTCGAGTGCGGCCGC TTACAGTCTTATTGGCATGA-3′ Hphyδ1 6135′-CTGGAATTCTATCGTAAAGATTTGGACCAT-3′ Hphyδ2 6145′-CCGCTCGAGTGCGGCCGCGGGGTTAATGATTTTTTGAAT-3′ Hphyδ′1 6155′-CTGGAATTCAAAAACTCCAACCGCCTTATT-3′ Hphyδ′2 6165′-CCGCTCGAGTGCGGCCGCTGGCGTTTTCTTTTTGGATAA-3′ HylexA 6175′-CACTAAAGGGCGGCCGCATGAAAGCGTTAACGGCCAG-3′ Hpτ1 6185′-CGCCTCGAGATGCAAGTTTTAGCGTTAAAA-3′ Hpτ2 619 5′-CGAGGAGCCTCGAGTCATAACAATTCCACGCTTTTG-3′

[0212] To construct pET-Hpδ, pET-Hpδ′, and pET-Hpβ, we carried out PCRreactions using H. pylori J99 genomic DNA as template with the pair ofprimers Hpδ1 and Hpδ2, Hpδ′1 and Hpδ′2; and Hpβ1 and Hpβ2 respectively(Table 14). E. coli β was amplified from genomic DNA of strain XL-1Bluewith the primers Ecβ1 and Ecβ2 (Table 1). The resulting PCR fragmentswere digested with NdeI and NotI and cloned in the T7 promoter-based E.coli expression vector pET20b. The open reading frames (ORFs) of humanPCNA, H. pylori δ and δ′ contained no stop codon and were inserted infront of the C-terminal His₆ tag in pET20b vector. In plasmids pET-Hpβand pET-Ecβ, a stop codon was introduced before the NotI site andtherefore expressed the native (non-tagged) proteins. All inserts andcloning junctions sequenced using an Applied Biosystems sequencer.

[0213] In Vitro Binding Assay

[0214] Radiolabelled (³⁵S-labeled) proteins were produced from variouspET plasmids by in vitro transcription and translation using E. coli T7S30 extract (Promega) and [³⁵S] methionine (Amersham Pharmacia Biotech)according to the manufacturer's recommendations. RadiolabelledHis₆-tagged proteins (10-20 μl of the S30 extract reactions) wereincubated for 1 h at 4° C. with 50 μl of 50% slurry of Ni-NTA resin in atotal volume of 100 μl in binding buffer (50 mM NaH₂PO₄, 300 mM NaCl, 10mM imidazole, pH8). The Ni-NTA beads were washed twice in the washbuffer (50 mM NaH₂PO₄, 300 mM NaCl, 20 mM imidazole pH8) and thenresuspended in binding buffer BB14 (20 mM Tris pH 7.5, 0.1 mM EDTA, 25mM NaCl, 10 mM MgCl₂) and then incubated with [³⁵S]methionine-labelledβ. After 1 h incubation at RT, the beads were washed three times withthe WB3 buffer (20 mM Tris pH 7.5, 0.1 mM EDTA, 0.05% Tween20) andproteins bound on the Ni-NTA beads were eluted by the addition ofLaemmli sample buffer incubated for 5 min at 100° C. and were subjectedto SDS-PAGE gel electrophoresis. Radiolabelled proteins were visualizedby autoradiography with BioMaxTransScreen and BioMax MS film (Kodak).

[0215] Yeast Two-Hybrid System

[0216] Full-length ORFs of the H. pylori δ, τ and δ′ genes were obtainedby PCR using gene-specific primers with flanking EcoRI and XhoI (Table14). The PCR fragments were digested with EcoRI and XhoI and cloned intoboth pLexA and pB42AD vectors. Cloning into pLexA placed the H. pylori δand δ′ ORFs in frame with the DNA-binding domain of LexA, downstream ofthe ADH promoter. Cloning into pB42AD placed the H. pylori δ and δ′ ORFsin frame with the B42 transcription activator domain and the C-terminalhem agglutinin (HA) epitope tag. For simultaneous expression of theLexA-δ and unfused τ proteins, a modified two-hybrid vector pESCLexHpδ/τwas constructed as follows. The DNA fragment containing the LexA DNAbinding domain fused to the H. pylori δ ORF was PCR amplified fromplasmid pLexAHpδ using the primers HyLexA and Hyδ 2 containing the NotIsite, digested with Not I and inserted into the yeast dual expressionvector pESC-LEU (Stratagene) to obtain pESCLexAδ. Finally, the H. pyloriτ ORF was amplified by PCR using the primers Hyτ1 and Hyτ2 (Table 14),digested with XhoI and cloned into pESCLexAδ digested with XhoI. Theresulting plasmid, pESCLexAδ/τ, coexpressed the LexAδ fusion proteinfrom the yeast GAL10 promoter and the c-myc epitope tagged τ from theGAL1 promoter.

[0217] β-Galactosidase

[0218] Three to six transformants were patched onto selective medium andgrown for 1 day at 30° C. when they were inoculated and grown to mid-logphase in selective medium containing glucose or galactose as indicated.β-galactosidase activity was assayed using Yeast β-Galactosidase kit(Pierce) and expressed in Miller units.

[0219] Co-Immunoprecipitation and Western Blotting

[0220] Yeast cells were allowed to grow in 50 ml of minimal mediumcontaining 2% D(+) raffinose to an OD₆₀₀ up to 0.7 when shifted to amedium containing 2% D(+) galactose in order to induce Gal1/10 promoter.For protein extraction, yeast cells were harvested at OD₆₀₀ of 1.0(approximately 1×10⁷ cells/ml) and collected by centrifugation andresuspended in ice-cold lysis buffer (50 mM Hepes, pH 7.5, 150 mM NaCl,1.5 mM MgCl₂, 0.2 mM EDTA, 25% glycerol, 1 mM DTT) containing 2 mMphenylmethysulonyl fluoride and complete protease inhibitor cocktail(Boehinger Mannheim). Approximately ⅓ volume of ice-cold glass beadswere added, and the cells were broken by vortexing several times at 4°C. The lysed cells were centrifuged and the lysate transferred to a newtube. For co-immunoprecipitations, the lysates were incubated withspecific antibodies (anti-HA, 12A5 from Boehringer Mannheim) at 4° C.After 2 h, protein A-Sepharose (Amersham Pharmacia Biotech) was added,and the mixture was incubated for a further 2 h at 4° C. Theimmunoprecipitates were washed in ice-cold washing solution containing10 mM Tris-HCl, pH 7.0, 50 mM NaCl, 30 mM NaPP, 50 mM NaF, 2 mM EDTA and1% Triton X-100. Proteins were separated on 10% SDS-PAGE gels andtransferred to nitrocellulose membranes (Bio-Rad). The membranes wereblocked with 3% blotto in PBST (phosphate-buffered saline plus 0.1%Tween 20) for 1 h and subsequently incubated with either a anti-LexApolyclonal antibody or a anti-myc monoclonal antibody (Invitrogen) for 1h, washed in PBST, and incubated for 1 h with peroxidase-conjugatedsecondary antibody. The membranes were washed in PBST and developed withenhanced chemiluminescence (Pierce), followed by exposure to HyperfilmECL (Amersham Pharmacia Biotech).

B. Results

[0221] Identification of a Gene Encoding a Putative Orthologue of δ fromH. pylori

[0222] Initial BLAST searches of the translated complete genome sequenceof H. pylori J99 with the E. coli and H. influenzae δ amino acidsequences failed to identify any significant matches. However, after amore extensive reiterative series of searches a family of proteinsencoding putative orthologues of δ was identified. All bacteria withcompleted or substantially completed genome sequences contained a singlegene encoding a member of the family, but most of the members of thisfamily are currently not recognised as such. The alignment of theproposed orthologues of δ present in a range of bacteria with fullysequenced genomes is shown in FIG. 3. In FIG. 3, the amino acidsequences of the proposed degenerate AAA+ domain of the δ orthologuesfrom E. coli (Ec), Rickettsia prowazeki (Rp), H. pylori J99 (Hp),Mycobacterium tuberculosis (Mt), Bacillus subtilis (Bs), Mycoplasmapneumoniae (Mp), Borrelia burgdorferi (Bb), Treponema pallidum (Tp),Synechocysitis sp. (S), Chlaymdia pneumoniae (Cp), Deinococcusradiodurans (Dr), Thermotoga maritima (Tm) and Aquifex aeolicus (Aa),are shown. The bracketed number is the number of amino acids missingfrom the alignment. The experimentally determined secondary structure ofE. coli δ′ (Guenther et al., Cell (1997) 91:335-345) is shown, alongwith predicted secondary structure of E. coli δ determined usingPSIPRED, s—sheet and h—helix. The members of the family are quite poorlyconserved in amino acid sequence, with no amino acids being 100%conserved. The highly conserved positions are a glycine and aphenylalanine located close to the amino-terminus and an aspartic orglutamic acid and a lysine located close to the carboxy-terminus of theprotein (FIG. 3). Unlike the δ′ and γ/τ families the sites withconservative substitutions are fairly well distributed across the wholelength of the protein. The overall low level of conservation in such animportant component of the clamp loader is probably due the apparentabsence of enzymatic activities, with the δ subunit being primarilyinvolved in protein-protein interactions.

[0223] The proposed H. pylori δ orthologue is encoded by gene jhp1168.The predicted protein exhibited low amino acid identity to the E. coliδ.

[0224] His₆ Tagged Helicobacter pylori δ can Bind δ

[0225] In order to confirm the identification of the putative δorthologue in H. pylori, we first examined the interaction between H.pylori δ and the proposed β using an in vitro biochemical assay. VariousH. pylori proteins δ, δ′, β and human PCNA (the eukaryote equivalent ofthe β subunit of DNA Polymerase III), and β from E. coli were expressedin E. coli using pET plasmids. To verify the δ-β interaction we used aprotein interaction assays with one of the proteins immobilised onNi-NTA beads. Proteins were synthesised in vitro from pET plasmids usingE. coli T7 S30 extract and labelled with ³⁵S-methionine (FIG. 4). InFIG. 4A, proteins were synthesized by in vitro transcription-translationusing E. coli T7 S30 extract from various pET plasmids. Translationefficiency was estimated by parallel reactions in the presence of[³⁵S]Met. Aliquots (5 μl) of the reaction mixtures weresize-fractionated on 10% SDS/PAGE. The amount of proteins synthesizedwas quantitated by using a PhosphorImager and equal amounts were used inthe binding experiments. In FIG. 4B, ³⁵S-labeled His₆-tagged human PCNA(lanes 3 and 4), H. pylori δ (lanes 5 and 6), and δ′ (lanes 7 and 8)(5-15 μl of reaction mixtures) were immobilised on Ni-NTA agarose beads.The beads were washed and incubated with 10 μl of the S30 extractreaction mixture containing the ³⁵S-labeled H. pylori β or E. coli βprotein. Proteins associated with the resin were detected by SDS/PAGE on10% gels followed by autoradiography. Lanes 1 and 2 are controls wherereaction mixtures lacking plasmid template were used to bind Ni-NTAresin. The position of H. pylori β is indicated by an arrow. Each of the³⁵S-labeled and His₆-tagged proteins were separately immobilised toNi-NTA agarose beads via their His₆ tag. The Ni-NTA beads that carriedimmobilised S30 extract or each His₆-fusion proteins were washed andincubated with ³⁵S-labeled β protein. After washing, the ³⁵S-labeledproteins bound to the beads were eluted and analysed using SDS-PAGEfollowed by autoradiography. Typical results are shown in FIG. 4 anddemonstrate that H. pylori β only bound to His₆δ. The binding isspecific: H. pylori β did not bind to δ′ or to human PCNA. Moreover theinteraction is species specific since E. coli β did not bind to H.pylori His₆-δ.

[0226] δ and δ′ Interact in the Presence of τ

[0227] Next we tested the association among H. pylori clamp loadingproteins in formation of complex using the yeast two-hybrid system. Eachof the three H. pylori clamp loading proteins (δ, δ′ and τ) wasexpressed as a fusion with either a DNA-binding protein, LexA, or thetranscription activation domain of B42. β-galactosidase activity showedno interaction or weak interactions in doubly transformed yeast cellsthat expressed two types of fusion proteins (FIG. 5). In FIG. 5,EGY40[p8op-lacZ] was transformed with plasmids expressing LexA-δ andB42-δ′ and τ. Protein extracts were prepared from cells grown in 2%galactose in order to induce gene expression. Immunoprecipitationsperformed with anti-HA (12A5) antibodies. Cell lysates andimmunoprecipitates (IP) were analysed on immunoblotted with polyclonalanti-LexA antibody (A); immunoblotted with anti-myc antibody (B). Thepositions of LexA-δ (predicted molecular mass of 65 kDa) and τ predictedmolecular mass of 70 kDa) are indicated by arrows. We reasoned thatalthough the two-hybrid system can detect interaction between twowell-defined proteins, this method failed to detect interactions betweenproteins that are part of a larger protein complex such as the clamploader studied here. This may be due to the weak interactions whichexist between two members of the multi-protein complex. Therefore, weasked whether the presence of τ would enhance δ and δ′ interaction. Totest this in yeast cells, we introduced a third plasmid expressing τinto the system. Transformants that simultaneously expressed LexA-δ,B42-δ′ and unfused τ exhibited significantly higher β-galactosidaseactivity than those producing LexA and B42-δ′ (FIG. 6). In FIG. 6,plasmids were transformed into EGY[p8op-lacZ] in a variety ofcombinations and assayed for β-Galactosidase activity, expressed inMiller units. Negative control transformants that produced LexA-δ,unfused B42 and τ did not show β-galactosidase activity (results notshown). Similar results obtained when the two proteins LexA-δ and τ wereexpressed from the same vector (pESCLexAHpδ/τ). We also confirmed thatthe amount of LexA-δ and B42-δ′ hybrid proteins accumulated wereunchanged both in δδ′τ-expressing yeast cells and in δδ′-expressingyeast cells, as estimated by Western blots using anti-HA and anti-LexAantisera (results not shown). Thus the presence of τ is not likely toaffect the level of expression of stability of LexA-δ and B42-δ′proteins. The results show that δ and δ′ can interact in the presence ofτ.

[0228] Formation of a Clamp Loader (δδ′τ) Complex

[0229] Taken together, our results demonstrate that activation of thereporter gene transcription by the reconstituted activator LexA/B42results from the formation of a LexA-δ-B42-δ′ protein complex which ispromoted by a third partner in the clamp loader complex, τ. Such proteincomplexes can be visualized by immunoprecipitation from whole doubletransformed yeast cell extracts using antibodies directed towards the HAepitope of the B42-δ′ hybrid protein. Using anti-HA antibodies (12A5),we were able to immunoprecipitate not only LexA-δ but also τ from theyeast total cell extract (FIG. 5).

EXAMPLE 4

[0230] In this example, we identify the δ peptide motif responsible forthe interaction of the δ protein with β.

A. Methods

[0231] Analysis of the Amino Acid Sequences of the δ Family

[0232] Predicted secondary structures were determined using the PSIPREDand GenThrEADER servers at http://insulin.brunel.ac.uk/psipred and theJpred server at http://jura.ebi.ac.uk:8888/submit.html. Protein foldrecognition was carried out using the 3D_PSSM server v2.5.1 athttp://www.bmm.icnet.uk/˜3dpssm. Modelling of δ protein structure basedon the β′ structure was undertaken using the SWISS-MODEL server athttp://www.expasy.ch/swissmod/SWISS-MODEL.html and viewed usingSwissPdbViewer.

[0233] Construction of Expression of Plasmids and Mutagenesis.

[0234] Plasmids expressing E. coli δ with an N-terminal His₆-tag wereconstructed in pET20b (Novagen). The LF to AA mutation of His₆-δ wasintroduced using the site directed mutagenesis method (Quikchangemutagenesis kit, Stratagene) according to the manufacturer'sinstructions. The mutagenic primers used were:5′-GCCAGGCTATGAGTGCGGCTGCCAGTCGACAAAC-3′, (Seq. ID No. 620) and5′-GTTTGTCGACTGGCAGCCGCACTCATAGCCTGGC-3′. (Seq. ID No. 621)

[0235] Ni-NTA Co Immobilisation Assay

[0236] The in vitro His₆-tagged δ protein was allowed to bind to Ni-NTAresin in 200 μl of binding buffer (50 mM NaH₂PO₄, 300 mM NaCl, 10 mMimidazole, pH8) at 4° C. for 1 h. The Ni-NTA resin was then washed 3times with wash buffer (50 mM NaH₂PO₄, 300 mM NaCl, 20 mM imidazolepH8). In vitro transcribed-translated [³⁵S]-labelled β protein was addedto Ni-NTA resin in BB14 interaction buffer (20 mM Tris pH7.5, 0.1 mMEDTA, 25 mM NaCl and 10 mM MgCl₂) and allowed to bind for 1 h at RT. Theresin was then washed 3 times with WB3 buffer (20 mM Tris pH7.5, 0.1 mMEDTA, 0.05% Tween20). The bound proteins eluted by heating the resin for5 min at 100° C. in SDS-PAGE reducing sample buffer. [³⁵S]-labelledproteins were visualised by autoradiography.

B. Results

[0237] Domain Organisation of δ Family Proteins

[0238] During the PSI BLAST searches of the databases a substantialnumber of the hits of borderline significance with bacterial γ/τ andarcheal and eukaryotic clamp loader proteins (RFC subunits) andbacterial DnaA proteins in the region of these proteins that containsthe AAA+ domain were registered. The AAA+ domain is involved inATP-binding and is also proposed to be involved in subunitoligomerisation of many members of the extremely large family ofproteins that contain it (Neuwald et al., Genome Research (1999) 9:27-43). Many of these proteins are associated with the assembly,operation and disassembly of protein complexes (Neuwald et al., 1999).Given the role of δ in the clamp loader these similarities were exploredin more detail. On the basis of the alignments produced from the PSIBLAST and HMM searches and the nature of the conservation of residues,representative δ sequences were aligned with the AAA+ domain regions ofE. coli δ′ and γ/τ (FIG. 3). The predicted secondary structure of E.coli δ by two different methods is in good agreement with theexperimentally determined secondary structure features of E. coli δ′(FIG. 3). Furthermore, fold-recognition searches using the 3D-pssm foldrecognition server with the H. pylori, E. coli and Aquifex aeolicus δsequences identified matches to the E. coli δ′ structural folds withprobabilities of 0.13, 8.01e-07, 5.15e-06 and respectively, providingfurther support for the proposal that the amino-terminal region of δfolds into an AAA+ domain. T he most conserved residues in the AAA+family domain are those involved in the ATPase activity. Since δ, likeδ′, does not have ATPase activity we would not expect these residues tobe conserved. Rather we would expect conservation of residues thatcontribute to the secondary and tertiary structure of the domain. Goodconservation is seen for the core residues of the δ′ structure.

[0239] Despite extensive searching no significant relationships wereidentified between the carboxy-terminal regions of the δ orthologues andthe other clamp loading proteins from eubacteria, or with the clamploading proteins from eukaryotes, archea and bacteriophages, or with anyother proteins in the non-redundant protein database at GenBank.

[0240] Identification of β-Binding Site in δ

[0241] When the positions of the most conserved residues in δ weremapped on our structural model of δ, a phenylalanine conserved in the δfamily, but not elsewhere, located in the second half of the Box IV′preceding the Walker B box (FIG. 3) was identified. It mapped as exposedon a surface loop in a region of δ putatively independent ofinter-subunit interactions (FIG. 7). The other conserved amino acidswere in regions conserved in δ, γ/τ or another of the clamp loaders(FIG. 3). The conserved phenylalanine is part of a region with the looseconsensus sequence sLF[AG] (where s is a small amino acid) (Table 15)and which is a good candidate for a role in the binding of δ to β duringthe loading of β onto DNA. TABLE 15 Delta Protein Family Sequences Seq.ID Sequence No. Sequence name N-term Motif C-term  1 741 delta Aquifexaeolicus VF5 SEEEFYTALS ETSIF GGSKEKAVVI  2 740 delta Thermotogamaritima MSB8 KIDFIRSLLR TKTIF SNKTIIDIVN  3 1803 delta Chloroflexusaurantiacus J-10-f1 QLVAACE AHPFL AERRLVIVYD  4 739 delta Deinococcusradiodurans R1 VSAETLGPHL APSLF GDGGVVVDFE  5 738 delta Porphyromonasgingivalis W83 SVADIANEAR RFPMM GRRQLIVVRE  6 769 delta Bacteroidesfragilis NCTC9343 DVATVINAAK RYPMM SEHQVVIVKE  7 751 delta Cytophagahutchinsonii JGI NVSTILQNAR KYPMF SERQVVMVKE  8 737 delta Chlorobiumtepidum TLS TLGQIVSAAS EYPMF TEKKLVVVRQ  9 736 delta Chlamydiatrachomatis LQQELLSWTD HFGLF ASQETIGIYQ 10 735 delta Chlamydophilapneumoniae MPATLMSWTE TFALF QEHETLGIIH 11 733 delta Nostoc punctiformeATCC29133 AAIQALNQVM TPTFG AGGRLVWLIN 12 755 delta Anabaena sp. PCC7120AAIQALNQVM TPAFG AGGRLVWLMN 13 734 delta Synechocystis sp. PCC6803ATQRGLEQAL TPPFG SGDRLVWVVD 14 732 delta Prochlorococcus marinus MED4QIKQAFDEIL TPPLG DGSRVVVLKN 15 780 delta Prochlorococcus marinus MIT9313QASQALAEAR TPPFG SGGRLVLLQR 16 754 delta Synechococcus sp. WH8102QAAQALDEAR TPPFA SGERLVLLQR 17 1810 delta Treponema denticola TIGRGMGDVISLLQ NASLF SSAKLIILKS 18 731 delta Treponema pallidum NicholsPVADLVDLLR TRALF ADAVCVVLYN 19 730 delta Borrelia burgdorferi B31SAVGFAEKLF SNSFF SKKEIFIVYE 20 752 delta Magnetospirillummagnetotacticum IPSRLADEAA AMALG GGRRVVVLRD MS-1 21 753 deltaMagnetospirillum magnetotacticum DPGRLVDEAG TVGLF GGSRTIWVRS MS-1 22 706delta Rhodopseudomonas palustris CGA009 EPSRLVDEAL AIPMF GGRRAIRVRA 23778 delta Mesorhizobium loti MAFF303099 DEGRLLDEAR TVPMF SDRRLLWVRN 24743 delta Brucella suis 1330 DPAKLADEAG TISMF GGQRLIWIKN 25 1808 deltaSinorhizobium meliloti 1021 GAGSVLDEVN AIGLF GGDKLVWVRG 26 1809 deltaAgrobacterium tumefaciens C58 DPGRLLDEVN AIGLF GGEKLVWVKS 27 707 deltaCaulobacter crescentus TIGR DPAKLEDELS AMSLM GGRRLVRLRL 28 782 deltaRhodobacter sphaeroides 2.4.1 DPAALMDAMT AKGFF EGPRAVLVEE 29 1799 deltaRickettsia conorii Malish_7 NISSLEILLN SSNFF GQKELIKIRS 30 708 deltaRickettsia prowazekii Madrid_E NILSLDILLN SPNFF GQKELIKVRS 31 746 deltaWolbachia sp. TIGR SPSLLFSELA NVSMF TSKKLIKLIN 32 702 delta Neisseriagonorrhoeae FA1090 DWNELLQTAG NAGLF ADLKLLELHI 33 701 delta Neisseriameningitidis Z2491 DWNELLQTAG SAGLF ADLKLLELHI 34 703 delta Nitrosomonaseuropaea DWMNLFQWGR QSSLF SERRMLDLRI Schmidt_Stan_Watson 35 704 deltaBordetella pertussis Tohama_I DWSAVAAATQ SVSLF GDRRLLELKI 36 1807 deltaBurkholderia pseudomallei K96243 DWSTLIGASQ AMSLF GERQLVELRI 37 748delta Burkholderia cepacia LB400 DWSSLLGASQ SMSLF GDRQLVELRI 38 742delta Burkholderia mallei ATCC23344 DWSTLIGASQ AMSLF GERQLVELRI 39 749delta Ralstonia metallidurans CH34 QWGQVIEAQQ SMSLF GDRKIVELRI 40 699delta Acidothiobacillus ferrooxidans IWDALRDERD AGSLF AAQRVLLLRLATCC23270 41 700 delta Xylella fastidiosa DWQQLASSFN APSLF SSRRLIEIRL8.1.b_clone_9.a.5.c 42 698 delta Legionella pneumophila EWHVVLEETN NYSLFYQTVILTIFF Philadelphia-1 43 744 delta Coxiella burnetii HWQSLTQSFDNFSLL SDKTLIELRN Nine_Mile_(RSA_493) 44 745 delta Methylococcuscapsulatus TIGR SWSTFLEAGD SVPLF GDRRILDLRL 45 696 delta Pseudomonasaeruginosa PAO1 DWGLLLEAGA SLSLF AEKRLIELRL 46 697 delta Pseudomonasputida KT2440 DWGTLLQAGA SLSLF AQRRLLELRL 47 759 delta Pseudomonassyringae DC3000 DWGTLLQAGA SMSLF AERRLLELRL 48 750 delta Pseudomonasfluorescens Pf0-1 DWGTLLQAGA SMSLF AEKRLLELRL 49 695 delta Shewanellaputrefaciens MR-1 NWGDLTQEWQ AMSLF SSRRIIELTL 50 694 delta Vibriocholerae N16961 DWNAVYDCCQ ALSLF SSRQLIEIEI 51 690 delta Pasteurellamultocida Pm70 NWSDLFERCQ SIGLF FNKQILFLNL 52 691 delta Haemophilusinfluenzae KW20 DWAQLIESCQ SIGLF FSKQILSLNL 53 692 delta Haemophilusducreyi 35000HP KWEQLFESVQ NFGLF FSRQIIILNL 54 693 delta ActinobacillusDWNDLFERVQ SMGLF FNKQLIILDL actinomycetemcomitans HK1651 55 689 deltaBuchnera sp. APS DWKKIILFYK TNNLF FKKTTLVINF 56 685 delta Escherichiacoli MG1655 DWNAIFSLCQ AMSLF ASRQTLLLLL 57 686 delta Salmonella typhiCT18 DWGSLFSLCQ AMSLF ASRQTLVLQL 58 764 delta Salmonella typhimuriumDWGSLFSLCQ AMSLF ASRQTLVLQL 59 687 delta Klebsiella pneumoniae MGH78578PTGRRFSLKP GDELF ASRQTLLLIL 60 688 delta Yersinia pestis CO-92EWEHIFSLCQ ALSLF ASRQTLLLSF 61 763 delta Yersinia pseudotuberculosisEWEHIFSLCQ ALSLF ASRQTLLLSF IP32953 62 766 delta Desulfovibrio vulgarisLPPVFWEHLT LQGLF GSPRALVVRN Hildenborough 63 761 delta Geobactersulfurreducens TIGR KGDDIATAAQ TLPMF ADRRMVLVKR 64 710 deltaHelicobacter pylori EKSQIATLLE QDSLF GGSSLVILKL 65 709 deltaCampylobacter jejuni NCTC11168 NFTRASDFLS AGSLF SEKKLLEIKT 66 711 deltaStreptomyces coelicolor A3 (2) LQPGTLAELT SPSLF AERKVVVVRN 67 767 deltaThermobifida fusca YX VSAGKLVEVT SPSLF GDRRVVVLRS 68 713 deltaMycobacterium avium 104 VSTYELAELL SPSLF AEERIVVLEA 69 714 deltaMycobacterium leprae TN VGTYELTELL SPSLF ADERIVVLEA 70 762 deltaMycobacterium smegmatis MC2_155 VSTSELAELL SPSLF AEERLVVLEA 71 712 deltaMycobacterium tuberculosis H37Rv VGAYELAELL SPSLF AEERIVVLGA 72 715delta Corynebacterium diptheriae VNASELIQLT SPSLF GEDRIIVLTN NCTC1312973 716 delta Dehalococcoides ethenogenes TIGR TAAELQNYVQ TIPFLAPARLVMVNG 74 1806 delta Clostridium difficile 630 VLNHLISSIE TLPFMDDRKI 75 758 delta Carboxydothermus hydrogenoformans LPEEVVARAE TVSFFGQRFIVVKNC TIGR 76 721 delta Bacillus halodurans C-125 PIEAALEEAE TVPFFGSKRVVILKD 77 717 delta Bacillus stearothermophilus 10 PIEAALEEAE TVPFFGERRVILIKH 78 718 delta Bacillus subtilis 168 PLDQAIADAE TFPFMGERRLVIVKN 79 719 delta Staphylococcus aureus COL EIAPIVEETL TLPFFSDKKAILVKN 80 760 delta Staphylococcus epidermidis RP62A DLTPIIEETLTMPFF SNKKAIVVKN 81 720 delta Bacillus anthracis Ames YLEDVVEDAR TLPFFGERKVLLIKS 82 1800 delta Listeria innocua Clip11262 PIEVVIQEAE SMPFFGDKRLVMANN 83 1802 delta Listeria monocytogenes 4b PIEVVIQEAE SMPFFGDKRLVMANN 84 1801 delta Listeria monocytogenes EGD-e PIEVVVQEAE SMPFFGDKRLVMANN 85 722 delta Enterococcus faecalis V583 PLSAAIAEAE TIPFFGDYRLVFVEN 86 756 delta Enterococcus faecium DOE SLDEVVAEAE TLPFFGDQRLVFVEN 87 765 delta Lactococcus lactis IL1403 NSDLALEDLE SLPFFSDSRLVILEN 88 757 delta Streptococcus equi Sanger LYQTAEMDLV SMPFFADQKVVIFDH 89 723 delta Streptococcus agalactiae DYQNAELDLE SLPFLSDYKVVIFDQ 90 724 delta Streptococcus pyogenes M1_GAS AYQDAEMDLV SLPFFAEQKVVIFDH 91 747 delta Streptococcus mutans UA159 SYQDAEMDLE SLPFFADEKIVIFDN 92 1804 delta Streptococcus gordonii DYQQVELDLV SLPFFSDEKIIILDH 93 725 delta Streptococcus pneumoniae type_4 VYKDVELELV SLPFFADEKIVILDY 94 726 delta Ureaplasma urealyticum Serovar_3 SLISFKNLIEQDDLF NSNKIYLFKN 95 728 delta Mycoplasma genitalium G-37 KDLKQLYDLFSQPLF GSNNEKFIVN 96 727 delta Mycoplasma pneumoniae M129 DVNKLYDVVLNQNLF AEDTKPILIH 97 1805 delta Mycoplasma pulmonis EIDDLLNDIV QKDLFSPNKIIHIKN 98 729 delta Clostridium acetobutylicum EFEDILNACE TVPFMSEKRMVVVYR ATCC824D

[0242] To determine whether the proposed LF peptide motif constitutespart of the β binding site, mutant δ was made by substituting LF with AA(2 alanine). When the AA mutant protein was used in Ni-NTA coimmobilisation assay, it did not bind to β (FIG. 8). In FIG. 8, aliquotsof 5-15 μl of in vitro transcribed and translated β protein was allowedto bind to immobilized His₆-tagged wild type δ or mutant δ (δ_(AA)). Thebound proteins were eluted and applied to SDS-PAGE; 5 μl of inputproteins shown in the figure. E. coli, δ-β interaction was clearlydisrupted by altering the LF to AA, further demonstrating the importanceof this motif for interaction with β (FIG. 8).

EXAMPLE 5

[0243] In this example, we present a model for the binding of thepeptide motif identified and characterised in the above examples toeubacterial δ proteins.

A. Methods

[0244] The 3D structure of a subunit of PCNA from PDB coordinate file1AXC and a subunit of β from PDB coordinate file 2POL from the RCSBProtein Data Bank (http://www.rcsb.org/pdb/index.html) were superimposedusing Deep View (http://www.expasy.ch/spdbv/mainpage.htm). Thecoordinates of the p21 peptide binding to the chosen subunit of PCNAwere then merged with the coordinates of β to create a coordinate filecontaining the coordinates of a subunit of β and of the p21 peptide. Thecoordinates of amino acids 144 to 148 of the p21 peptide were retainedand the rest removed. The five amino acids remaining were mutated togive the peptide QLSLF (Seq. ID No. 622) and the coordinates resaved.These coordinates were the starting point for sixty energy minimisationruns using the flexible docking mode in the InsightII package(Accelrys). The final minimized structures were compared and the fivelowest energy structures with the position of the amino-terminalglutamine in a similar position to the starting structure were chosenfor further analysis.

B. Results

[0245] Modelling Binding of QLSLF Peptide to β

[0246] Mutations in the carboxy-terminus of E. coli β have been shown toreduce the binding of δ to β (Naktinis et al, Cell (1996) 84: 137-145).The nature of the conserved β-binding motifs demonstrated that the majorinteractions between the β-binding peptide and β where hydrophobic innature. The structure of β has been determined and deposited in theProtein Database with the code 2POL (Kong et al., Cell (1992) 69:425-437). The region of the surface of β in the vicinity of thecarboxyl-terminus was analysed for hydrophobic areas. Two such pocketswere identified. The amino acids contributing to the two pockets in allof the available sequences of eubacterial β proteins are listed in Table16. TABLE 16 Phylogenetic variation in the residues proposed tocontribute to the hydrophobic pockets on β to which the β-bindingpeptide binds Position (numbered according to E. coli sequence) Species170 172 175 177 241 242 247 346 360 362 Escherichia coli V T H L F P V SV M Salmonella typhi V T H L F P V S V M Salmonella typhimurium V T H LF P V S V M Yersinia pestis V T H L F P V S V M Proteus mirabilis V T HL F P V S V M Buchnera aphidicola 1 V T Y L Y P V S V M Buchneraaphidicola 2 V T Y L Y P I S V M Buchnera aphidicola 3 V T Y L Y P V S VM Buchnera aphidicola 4 V T Y L Y P I S V M Buchnera aphidicola 5 V T YL Y P I S V M Pasteurella multocida V T H L F P V S V M Haemophilusinfluenzae V T H L F P V S V M Vibrio cholerae V T H M F P V S V MShewanella putrefaciens I T H L F P V S V M Pseudomonas aeruginosa V T HL F P V S V M Pseudomonas putida V T H L F P V S V M Legionellapneumophila V T H M F P A S I M Thiobacillus ferroxidans V T H L Y P V SI M Neisseria gonorrheae V T H L F P V S I M Neisseria meningiditis V TH L F P V S I M Nitrosomonas europea V T H L F L A S V M Bordetellabronchiseptica V T H L F P V S V M Bordetella pertusis V T H L F P V S VM Rickettsia prowazekii A T Y L F P F S V M Caulobacter crescentus V T HL F P V P V M Campylobacter jejuni V T K L F P V A I M Helicobacterpyloris J99 V T K L Y P I P L M Helicobacter pylori 26695 V T K L Y P IP L M Streptomyces coelicolor A T Y F L P L P L M Mycobacterium avium AT F L F P L P L M Mycobacterium bovis A T F L F P L P L M Mycobacteriumleprae A T F L F P L P L M Mycobacterium smegmatis A T F L F P L P L MBacillus subtilis T T H L Y P L P L L Staphylococcus aureus T T H L Y PL P L L Bacillus anthracis I T H L Y P L P L L Bacillus halodurans T T HL Y P M P L S Lactococcus lactis V T H M Y P L P L T Streptococcuspyogenes V T H M Y P L P L T Streptococcus mutans V T H M Y P L P L TStreptococcus pneumoniae V T H L Y P L P L T Streptococcus pneumoniae 2V T H L Y P L P L T Mycoplasma capricolum S T F I F P A P V LSpiroplasma citri T T F L Y P V P L L Ureaplasma urealyticum I T I A Y PI P I S Mycoplasma genitalium E S Y L F P F Y I V Mycoplasma pneumoniaeE S Y L F P L Y I V Clostridium acetobutylicum V I Y L F I I P L LTreponema pallidum V T K L F P V A I M Borrelia burgdorferi V T H M Y PI K L M Synechocystis PCC7942 A T H L Y P L P L M Synechocystis sp A T HL Y P L P L M Prochlorococcus marinus A T H L Y P L P L M Chlamydophilapneumoniae V T K L F P V P V M Chlamydia pneumoniae AR39 V T K L F P V PV M Chlamydia trachomatis V T K L F P V P V M Chlamydia muridarum V T KL F P V P V M Chlorobium tepidum V T H L Y P V A L M Porphyromonasgingivalis V S Q L Y P V A L L Deinococcus radiodurans V S Y V F P V P LR Thermotoga maritima V S R L F P V P I M Aquifex aeolicus V S H L F P VA I M

[0247] Modelling of the QLSLF (Seq. ID No. 622) consensus peptide intothis region indicated that these amino acids were likely to contributeto the binding of the β-binding peptides to β. Therefore these aminoacids constitute that part of the surface of β which interacts with theβ-binding peptides.

EXAMPLE 6

[0248] A number of peptide analogues of the β protein-binding motif weretested for their ability to inhibit the binding of the replisomalproteins α and δ to β. The results of these experiments follow.

A. Methods

[0249] Plate Inhibition Assays

[0250] Recombinantly expressed wild type E. coli α subunit was purifiedand coated onto 96 well microtitre plates (Falcon flexible plates,Becton Dickinson) at 20 μg/ml in 100 mM Na₂CO₃, pH9.5 (50 μl/well, 4° C.overnight or 2 h, RT (RT). The plates were washed in WB3 (20 mM Tris (pH7.5), 0.1 mM EDTA containing 0.05% v/v Tween 20). This buffer was usedin all wash steps through out the assay. The plates were then blockedwith “blotto” (5% skim milk powder in WB3, 100 μl/well, RT) untilrequired. Immediately before use the plates were washed.

[0251] The purified synthetic peptides and β subunit were diluted inBB14 (20 mM Tris, pH 7.5, 10 mM MgCl₂, 0.1 mM EDTA). Purified syntheticpeptides with concentrations of 9.3-300 and 1000 μg/ml were allowed tocomplex with purified wild type β subunit (5 μg/ml) in a 96 wellmicrotitre plate (Sarsted, Adelaide, Australia) pre-treated with“blotto” (30 min, RT). The reaction volume was 120 μl. The β subunitalso was incubated in the absence of peptide or in the presence of the αsubunit at 76.5 (μg/ml in BB14. All samples were incubated for 1 h (RT).Two 50 μl samples were transferred from each well to a correspondingwell of the washed and “blocked” α subunit coated plates, and furtherincubated for 30 min (RT).

[0252] The plates were washed and treated with rabbit serum raised tothe β subunit. The anti-serum was diluted 1:1000 in WB3 containing 10%“blotto”, dispensed at 50 μl/well and incubated for 12 min (RT). Theplates were washed again and treated with sheep anti-rabbit Ig-HRPconjugate (Silenus, Melbourne, Australia) diluted 1:1000 in WB3containing 10% “blotto” (50 μl/well). The plate was incubated for 12 min(RT). After a final washing step, 1 mM 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) was added (110 μl/well). Colourdevelopment was assessed at 405 nm using a plate reader (MultiskanAscent, Labsystems, Sweden).

[0253] The δ-β plate binding assay followed a similar regime but withthe following changes: purified wild-type E. coli δ subunit was coatedonto the plate at 5 μg/ml; the same concentration of synthetic peptideswere preincubated with the β subunit at 1 μg/ml; and the pre-formedpeptide-complexes were transferred to the δ subunit coated plates andincubated for only 10 min.

B. Results

[0254] Several nine amino acid peptides with sequences based on theamino acid sequence containing the QxSLF motif in DnaE were synthesisedand purified. The peptides and their sequences are listed in Table 17.TABLE 17 Results of peptide inhibition assays Seq. ID IC₅₀ μg/ml PeptideNo. Sequence α δ DnaE 640 IG QADMF GV 14.6 218 pep1 641 IG QLDMF GV 2.812.9 pep2 642 IG QASMF GV 860 ni^(a) pep3 643 IG QADAF GV ni ni pep4 644IG QADMA GV ni ni pep5 645 IG QAVMF GV nd^(b) ni pep6 646 IG PADMF GV nini pep7 647 IG KADMF GV ni ni pep8 648 IG QADKF GV ni ni pep9 649 IGQADMK GV ni ni pep11 650 IG QAAMF GV ni ni pep12 651 IG AADMF GV ni nipep13 652 IG QLSLF GV 1.42 9.5 pep14 653 IG QLDLF GV 1.33 8.8 pep15   QLD ni ni pep16    DLF 135 1200

[0255] Five nonapeptides, DnaE, and peptides 1, 2, 13, and 14 producedsignificant inhibition of the binding of α to β (Table 17). The sequencerelated nonapeptides 3 to 12 did not cause any inhibition of α:βbinding. Peptides 1, 13, 14 and DnaE also inhibited the binding of δ toβ. (Table 17). All other nonapeptides did not significantly inhibit βbinding.

[0256] Peptide Assays

[0257] We have demonstrated that specific peptides of nine amino acidscan bind to β and prevent binding of both αand δ to β, thus confiningthe limited extent of the residues required for interaction with β.These results also validate the assays for use in the screening forcompounds that interfere with the binding of α and/or δ to β, byproviding further evidence that the interactions being assayed arelikely to be similar to if not identical to the interactions in cells.

EXAMPLE 7

[0258] Design of a Tripeptide Inhibitor of α:β and δ:β Protein-ProteinInteractions.

[0259] In order to design smaller inhibitors of the interaction betweenproteins containing the β-binding peptides and β, the variation in thesequences of the β-binding peptides and the binding inhibition assaydata was examined in detail. The highest level of conservation observedwas for the amino acids in positions one, four and five (FIG. 9).

[0260] More than 70% of the peptide sequences (excluding δ) containedleucine in position four and phenylalanine in position five. The highlevel of conservation of the LF motif showed that these amino acids aremajor determinants of the interactions between β-binding proteins and β.The mutagenesis and peptide inhibition experiments confirm theimportance of the LF motif with the following importance of conformingto the consensus, position 5=4>1>3>2. However, positions 2 and 3modulate the interaction of the peptides with β. Substitution of thealanine at position two with leucine to generate peptide 2 substantiallyimproves competitiveness, whilst substitution of the aspartic acid atposition three with serine, to generate peptide 2 substantiallydecreased the competitiveness of the peptide. These results predictedthat the tripeptide DLF would inhibit binding of α and δ to β, but thetripeptide QLD although containing favoured amino acids was unlikely toinhibit binding. The two tripeptides QLD and DLF were synthesised andpurified. As predicted DLF, inhibited α:β binding (Table 17) with 50%inhibition at approximately 135 μg/ml and δ:β binding with 50%inhibition at approximately 1200 μg/ml.

[0261] These observations indicate that the dipeptide LF and/or variantsthereof (such as MF and DLF) with additional substitutions in the regionof the backbone are lead compounds for the design of other compoundsable to disrupt the interaction between β-binding proteins and β.

EXAMPLE 8

[0262] In this example, we demonstrate that the tripeptide DLF, an invitro inhibitor of α:β and δ:β interactions, inhibits the growth ofBacillus subtilis.

A. Methods

[0263]B. subtilis IH 6140 was subcultured from a fresh plate into a 10ml tube containing 5 ml of Oxoid Mueller-Hinton broth (Oxoid code CM405Oxoid Manual 7^(th) edition 1995 pg 2-161). This culture was shaken at120 rpm at 37° C. for 21 h and then diluted in normal saline to 0.5McFarland Standard (NCCLS Performance standard for DilutionAntimicrobial Susceptibility Testing M7-A4 January 1997). Thissuspension was further diluted 1:5 in normal saline to form thebacterial starter culture. Peptides were tested at a final concentrationof 1 mg/ml in a flat bottom 96 well plate (Nunclon surface, sterileNalge Nunc International). Wells were prepared by using 100 μl of doublestrength Mueller-Hinton Broth, an appropriate volume of peptide and thefinal volume made up to 190 μl. The wells were then inoculated with 10μl of the starter culture.

[0264] The plate was sealed with a clear adhesive plate seal (AbgeneHouse). It was then placed in a Labsystems Multiskan Ascentspectrophotometer. The plate was incubated at 37° C. with shaking at 120rpm every alternate 10 seconds. The absorbence at 620 nm was measuredevery 30 min for 16 h.

B. Results

[0265] The tripeptide DLF significantly inhibits the growth of B.subtilis, primarily by increasing the lag phase but also by decreasingthe growth rate during the following log phase (FIG. 10). In FIG. 10,the effect of tripeptides on the growth of B. subtilis is graphed asOD₆₂₀ against time of incubation. In contrast, the tripeptide QLD, whichdid not inhibit the interaction of α and δ with β, did not increase thelag phase but did decrease the growth rate during the log phase (seeFIG. 10 and Table 18). TABLE 18 Effect of DLF on growth of B. subtilisIncrease in Doubling time lag phase log phase Addition (Min) (Min) None— 125 QLD — 151 DLF 120 187

EXAMPLE 9

[0266] In this example we directly demonstrate, by surface plasmonresonance (SPR), the binding of peptides to β protein.

A. Methods

[0267] Surface Plasmon Resonance

[0268] Reverse phase HPLC purified peptides (10 μg) were reacted with 1mg biotin-linker (6-(6-((biotinoyl)amino(hexanoyl) amino) hexanoic acid)sulphosuccinimidyl ester; Molecular Probes, Eugene, Oreg.) (20 mg/ml inDMSO) in 75 mM sodium borate (pH8.5) overnight (RT) with rotation. Thereaction mixture was separated using a Brownlee C18 cartridge (AppliedBiosystems Inc., Foster City, Calif.) and a gradient of 6-65%acetonitrile in 0.1% TFA delivered at 0.5 ml/min over 40 min by HPLC(Shimadzu, Japan). Biotinylated peptides that eluted later than thebiotin-linker and free peptide, were collected, vacuum dried and thendissolved in water. SPR was conducted on a Biacore 2000 usingstreptavidin derivitised flow cell surfaces (Biacore). All β subunit andfree peptide solutions were prepared in BB14 with 150 mM NaCl.

[0269] For the KD studies, the biotinylated peptides were loaded ontothe flow cell surfaces such that interaction with 0.5 μM β subunitproduced a response of 50-100 RU. Upon completion of injection, RUvalues quickly returned to baseline at 10 and 50 μl/min flow rates,therefore regeneration buffers were not required. The dissociation rates(KD) were determined using the RU values obtained at steady state for 15different concentrations of the β subunit over 10 nM to 5 μM (induplicate) for each biotinylated peptide attached to the flow cellsurface. The data was fitted to the 1:1 Langmuir model by theBioEvaluation software (Biacore).

[0270] For the solution affinity analyses, higher loadings of thebiotinylated peptides on the flow cell surfaces, and therefore high RU(700-1000), were established. Loading with peptide 4 generated anegative control surface. Since this peptide does not interact with theβ subunit, and RU values on interaction with solutions of β subunitcannot be obtained, the flow cell surface was loaded with the same molaramount of biotinylated peptide 4 as the maximum required for any otherbiotinylated peptide. In all data manipulations, the RU values of thissurface was subtracted from the RU values of the test surface. Acalibration curve of RU values generated at different concentrations ofthe β subunit over 10-100 nM was developed for each biotinylated peptideattached to the flow cell surface. To determine the inhibitory effect offree peptide, 100 nM β subunit was pre-incubated for 5 min withdifferent concentrations of free peptide (10 nM to 4.5 μM, in duplicate)to form a complex of β subunit and peptide and then passed over the flowcell surfaces. The amount of free uncomplexed βremaining was determinedfrom the calibration curve. The log of the concentration of theuncomplexed (free) β subunit was plotted against the log concentrationof inhibitory peptide. From these plots, the IC₅₀ value, which in thiscase is the concentration of peptide required to complex 50 nM βsubunit, was determined.

B. Results

[0271] Binding curves exhibited rapid off- and on-rates, the latter toofast to determine by SPR. The KD was determined by fitting data to the1:1 Langmuir model (Table 19). As anticipated from previous bindingexperiments, the DnaE peptide returned the highest KD, 2.7 μM, whereaspeptide 1 returned the lowest KD, 500 nM. Peptides 13 and 14 gave verysimilar values, 778 and 800 nM, respectively.

[0272] To further differentiate the peptides, the IC₅₀ values ofpeptides 1, 4, 13 and 14 were determined in competition withbiotinylated peptides 1, 4 and 14 attached to flow cell surface bysolution affinity analysis. The peptide 4 surface was used as a negativecontrol. The IC₅₀ values for each peptide competing against biotinylatedpeptides 1 and 14 attached to the flow cell surface are listed in Table19. TABLE 19 Summary of kinetic parameters obtained by SPR IC₅₀ PeptideKD β-peptide 1¹ β-peptide 14 DnaE peptide  2.7 μM n.d.² n.d. Peptide 1 558 nM  920 nM  1.01 μM Peptide 4 n.d. >>10 μM  >>10 μM Peptide 13  800nM  440 nM   550 nM Peptide 14  778 nM  400 nM   500 nM

[0273] The results presented in Table 19 indicate that peptides 13 and14 are better competitors for the β subunit in solution than peptide 1,and that peptide 14 is slightly better than peptide 13.

EXAMPLE 10

[0274] In this example we alter the structure of a peptide and assay forinhibition of binding of α to β, demonstrating that some modificationsof the peptide do not alter activity.

A. Methods

[0275] A peptide with modified amino and carboxy-termini was synthesizedand assayed for its ability to inhibit the interaction of α with β. Thepeptide was synthesised and assayed as described in Example 6.

B. Results

[0276] The results presented in Table 20 show that acetylation of theamino-terminus and amidation of the carboxy-terminus of DLF had nosignificant impact on its ability to inhibit binding of α to β (comparethe results for peptides 16 and 18). TABLE 20 Peptide Sequence IC₅₀ α:β(μM) pep16 DLF 135 pep18 Ac-DLF-NH₂ 135

EXAMPLE 11

[0277] In this example we use the modelled structures of QLSLF (Seq. IDNo. 622) bound to β, derived in Example 5, and the experimental resultsfrom Example 6 as the basis for virtual screening of libraries ofchemicals. The example demonstrates a method for identification ofmimetics of components of the β-binding peptides based on the sequenceinformation derived from the bioinformatics and experimental analysis.

A. Methods

[0278] The structures of QLSLF (Seq. ID No. 622) and the substructuresSLF and LF extracted from the results of the modelling were used tosearch the NCI (National Cancer Institute) compound database(http://129.43.27.140/ncidb2/) using the “simple screen test” andvarious levels of “tanimoto index” options of the similarity search. Inaddition, DLF generated by mutating the S to D in QLSLF (Seq. ID No.622) using the following site was also used:

[0279] Deep View (http://www.expasy.ch/spdbv/mainpage.htm).

B. Results

[0280] A number of compounds were identified in each of these screens.Representative compounds are included in the tables referred to inExamples 13 and 14 below.

EXAMPLE 12

[0281] In this example we used the consensus sequence of β-bindingpeptides, derived in Example 1 and the experimental results from Example6 as the basis for virtual screening of chemical libraries. The exampledemonstrates a second method for identification of mimetics ofcomponents of the β-binding peptides based on the sequence informationderived from the bioinformatics and experimental analysis.

A. Methods

[0282] The sequences SLF and DLF were used to search the PDB databasefor the occurrence of these sequences in proteins with determined 3Dstructures. The substructures were removed from the files andsuperimposed to generate pharmacophore models of SLF and DLF usingcomponents of the Tripos suite of Cheminformatics programs (TriposInc.). The pharmacophore models were then used to search the NCI and CMS(CSIRO Molecular Science) libraries of compounds.

B. Results

[0283] As in the previous example, a number of compounds were identifiedin each of these screens. Representative compounds are included in thetables referred to in Examples 13 and 14 below.

EXAMPLE 13

[0284] In this example, we present the results of the testing of anumber of the chemical compounds identified in Examples 11 and 12 fortheir ability to inhibit the interaction of α and δ with β anddemonstrate that some chemical mimetics of components of the β-bindingpeptides do inhibit the interactions.

A. Methods

[0285] Compounds with high similarity scores, or at the intersection ofthe results of searches using a number of different approaches, andavailable from the NCI or CMS libraries were obtained and screened asdescribed in Example 6. For the CMS compounds in the of α:β assays,buffer BB37 replaced buffer BB14. Buffer BB37 contains 10 mM MnCl₂instead of the 10 mM MgCl₂ used in BB14. The buffer conditions werechanged to improve the reproducibility and sensitivity of the α:βbinding assay.

B. Results

[0286] Eleven NCI compounds and twenty CMS compounds were screened fortheir ability to inhibit the interaction of α and δ with β. Threecompounds with significant inhibition of either of the two bindingassays were identified. One of the compounds, 131123, significantlyinhibited the interaction of α with β, and two, 33850 and AOC-07877significantly inhibited the interaction of δ with β (see Table 21below). Thus, chemical mimetics of components of the β-binding peptidescan inhibit the binding of E. Coli α and δ to E. coli β. The compoundshave the following structures: TABLE 21

131123

338500

AOC-07877 Results of Chemical Compound Screen Compound Origin IC₅₀α-binding (μM) IC₅₀ δ-binding (μM) 23336 NCI Insoluble insoluble 125176NCI Partially insoluble Partially insoluble 131115 NCI >1000 >1000131123 NCI 210 >1000 131127 NCI >1000 >1000 163356 NCI >1000 >1000338500 NCI >1000 146 343030 NCI >1000 >1000 350589 NCI >1000 >1000353484 NCI >1000 >1000 400883 NCI >1000 >1000 AOC-04852 Molsci >300 >300AOC-05646 Molsci >300 inf AOC-05159 Molsci >300 >300 AOC-06097Molsci >300 inf AOC-06099 Molsci >300 >300 AOC-06240 Molsci >300 >300AOC-07182 Molsci >300 >300 AOC-05020 Molsci >300 inf AOC-07499Molsci >300 inf AOC-07877 Molsci 270 90 AOC-08944 Molsci >300 >300DCP-31462 Molsci 800 >1000 DCP-31461 Molsci 300 560 DCP-31458 Molsci 365500 DCP-31451 Molsci >1000 >1000 DCP-31448 Molsci >1000 >1000 DCP-31452Molsci >1000 >1000 DCP-31446 Molsci >1000 560 DCP-31444 Molsci >1000 650AOC-05203 Molsci 365 310

EXAMPLE 14

[0287] In this example we illustrate the screening of a number of thechemical mimetics identified in Examples 11 and 12 of components of theβ-binding peptides for their ability to inhibit the growth of bacteria.

A. Methods

[0288] Compounds with high similarity scores, or at the intersection ofthe results of searches using a number of different approaches, andavailable from the NCI or Molecular Science libraries were obtained andscreened for inhibition of growth of E. coli ATCC 35218, Klebsiellapneumoniae ATCC 13885, Pseudomonas aeruginosa ATCC 27853, Staphylococcusaureus ATCC 25923 and Enterococcus faecalis ATCC 33186 as follows.Compounds were supplied dissolved in DMSO at 1 mg/ml in a 96 well trayformat. Six corresponding slave plates were prepared by adding 85 μl ofsterile water, and 100 μl of two times Muller Hinton broth. Dissolvedcompounds (5 μl) from the master plate was added to the correspondingwell in slave plates giving a final concentration of 50 μg/ml.

[0289] Plates were then transferred to a PC2 Laboratory for inoculationwith selected bacterial strains. The strains are freshly grown anddiluted in normal saline to 0.5 McFarland Standard (NCCLS Performancestandard for Dilution Antimicrobial Susceptibility Testing M7-A4 January1997). This solution was further diluted 1:10 in normal saline to formthe bacterial inoculation culture. 10 μl was used to inoculate eachwell. Plates were covered and placed in a 35° C. incubator over nightbefore A₆₂₀ was determined. Tetracycline was used as a standardantimicrobial compound.

B. Results

[0290] Sixty three compounds from the CMS library were screened and twocompounds were identified that significantly inhibited the growth ofbacteria Specifically, compounds AOC-07877 and AOC-08944 both inhibitedthe growth of S. aureus and E. faecalis by more than 50% (see Table 22below in which the values shown are percent growth inhibition). Theformer compound also exhibited a significant inhibitory activity on theinteraction of δ and β. These results demonstrate the utility of theapproaches described for the identification of chemical leads usingpeptide sequence data to search chemical diversity for mimetics ofpeptides. TABLE 22 Effect on Bacterial Growth of Selected ChemicalCompounds. Test Conc Number Database μg/ml E. coli K. pneumoniae P.aeruginosa S. aureus E. faecalis 07337 molsci 30 −3 −7.8 4.9 −1.4 11.507262 molsci 32.5 3 −8.1 2.1 6.6 42.9 07497 molsci 25 19.6 11.5 10.910.8 35.7 07336 molsci 35 2.1 −2.9 4.6 6.7 42.9 07654 molsci 37.5 7.80.3 7.3 −3.1 14.4 07263 molsci 30 7.6 −4.5 5.9 −19.2 31.5 07499 molsci37.5 19.4 5.5 −2 75.1 9.5 07338 molsci 35 18.1 12 3.5 −6.2 17.6 08366molsci 32.5 11.2 4.6 −3.6 13.3 −67.2 08271 molsci 25 16.9 5.5 1.1 −15.3−31.4 07336 molsci 32.5 17.1 5.6 3.4 −24.3 −42.4 08462 molsci 25 15.4−70.5 −4.8 −39.2 −585 08270 molsci 27.5 10.9 −12.4 −1.8 −19.7 −70.907244 molsci 27.5 3.5 7.9 −0.7 −23 31.7 07409 molsci 32.5 8.7 11.1 3.9−110.6 73.5 07875 molsci 32.5 25 20.2 5.9 −24.4 36.9 07493 molsci 27.5−16.2 −2.1 3 −36.8 22.2 07245 molsci 27.5 4.8 −7.8 0.3 −23.7 18.8 07179molsci 37.5 −2 −6.3 3.7 −43.1 2.8 07494 molsci 32.5 6.6 −17.1 −1.8 −77.5−4.6 07492 molsci 25 −4.1 9.3 1.2 −58.5 −8 09623 molsci 35 5.5 −1.7 −0.8−27.1 32.5 09392 molsci 32.5 10.3 −13 0.3 −94.4 66.8 09102 molsci 25 1.9−21 0.9 29.9 15.8 09099 molsci 27.5 0.5 −23.1 −6 22.7 −2.4 08179 molsci30 3.9 −35.8 1.1 −13.3 −122.7 09427 molsci 27.5 2.3 10.2 −5.1 −35.9 21.908180 molsci 37.5 7.8 37.5 3.9 −21.3 154.6 07182 molsci 30 5.4 2.6 −15.8−45.9 −6 10041 molsci 35 8.4 17.7 −6.1 −51.5 11.9 07876 molsci 25 1.4−5.5 −9.9 20.6 12.5 07495 molsci 25 4 8.9 −0.3 10.9 −2 07877 molsci 3517.6 8.3 3.9 84.7 59.6 10040 molsci 35 11.8 7.4 4.5 −10.6 8 07496 molsci27.5 3.8 20.5 2.7 5.9 14.4 08944 molsci 25 10.5 9.5 13.5 101.8 87.110162 molsci 35 0.1 5.9 −0.6 35 5.2 10114 molsci 32.5 6.7 −9.4 2.5 −43.4−71.4 10038 molsci 30 13.5 −12.4 4.6 −11.7 −0.4 10115 molsci 25 24.3−17.1 15.2 −23.4 3.4 06097 molsci 35 8.6 −19.5 −3.5 −19.9 50.2 05155molsci 27.5 −4.2 8 7.9 22.1 −33.2 06099 molsci 25 18.4 9.3 1.4 5.9 −15.806242 molsci 32.5 7.9 5.2 12.3 11.9 −4.3 05023 molsci 37.5 −0.9 6.7 7.719.4 −148.8 05099 molsci 25 5.6 1.2 4.6 26.8 −79.7 05161 molsci 35 7.514.8 13.7 3 −5.1 06572 molsci 25 6 5.9 9 −27.8 −67.9 05098 molsci 30−1.4 9.7 11.3 14.2 −28.2 05154 molsci 25 −3.2 8.5 0 5.9 −20.4 04807molsci 32.5 −3.6 10.8 −5.4 53.1 1.7 05638 molsci 25 −4.6 9.3 5.5 17.6−39.5 05159 molsci 25 −5.7 16.9 1.9 13.5 −39.5 05001 molsci 37.5 1.4 8.511.8 47.1 −11.6 05020 molsci 35 6.9 25.9 −4.1 70.8 14 04852 molsci 27.5−3.5 8 3.2 38.9 −19.9 06240 molsci 27.5 −0.4 7.8 −2 39.1 −25.5 06243molsci 25 −1.9 8.7 4.5 28.7 −23.4 05158 molsci 35 −2.8 10 0.2 −12.7 −8.905646 molsci 25 4.2 13.7 −3.5 22.1 −17.2 06239 molsci 35 3.3 −4.7 −7.940.4 −54.9 11230 molsci 32.5 −2.7 1.3 9.9 −4.7 −14.1 04380 molsci 30−3.3 −21 8.8 −4.6 16

[0291] The structure of compound AOC-08944 follows:

EXAMPLE 15

[0292] In this example we illustrate the screening of representatives ofa library of compounds for their ability to inhibit the binding of E.coli α to E. coli β.

A. Methods

[0293] Compounds from the CMS library were dissolved in DMSO at 1 mg/mlin a 96 well tray format. A corresponding slave plate was prepared byadding 115 μl of BB37. Dissolved compounds (5 μl) from the master platewas added to the corresponding well in slave plates giving a finalconcentration of 41.7 μg/ml.

[0294] Compounds were assayed for inhibition of the binding of E. coli αto E. coli β as described in Example 13.

B. Results

[0295] Sixty compounds from the CMS library were screened. One compound(AOL-06454: see structure below) was identified that significantlyinhibited the binding of E. coli α to E. coli β. TABLE 23 Inhibition ofBinding of E. coli α To E. coli β of a Chemical Compound Number DatabaseTest Concentration % Inhibition AOC-06454 molsci 41.7 υg/ml 96 υM 72.2,75.3

AOC-06454

[0296] The foregoing result demonstrates that the assays as describedare suitable for the screening of large libraries of chemical compoundsfor compounds that inhibit the interaction of E. coli α and β.

EXAMPLE 16

[0297] In this example, we describe the screening of additional peptidesfrom E. coli β-binding proteins for their ability to inhibit theinteraction of E. coli α and δ with E. coli β.

A. Methods

[0298] Peptides were assayed for inhibition of the binding of E. coli αto E. coli β as described in Example 6 with the exception that bufferBB37 replaced buffer BB14 in the alpha:beta binding assay. As notedabove, BB37 contains 10 mM MnCl₂ instead of 10 mM MgCl₂ used in BB14.Again, the change in buffer conditions was made to improve thereproducibility and sensitivity of the α:β binding assay.

B. Results

[0299] A number of peptides from E. coli proteins containing putativeβ-binding sites were assayed for their ability to inhibit theinteraction of E. coli α and δ with E. coli β. Some of the penta- andhexa-peptide motifs were flanked by the flanking sequences from E. coliα (peptides 110a-f, 112a and pep13) and some by their native flankingsequences (peptides 112c and d). TABLE 24 Inhibition of Binding of E.coli α to E. coli β by Peptides Source Peptide Seq. ID IC₅₀ α:β IC₅₀ δ:βProtein Number No. Sequence (μM) (μM) delta 110a 654 IGQAMSL FGV27.0 >100 DinB1 110b 655 IGQ LVLGLGV 9.3 6.8 DnaA2 110c 656 IGQ LSLPLGV3.4 3.3 UmuC2 110d 657 IGQ LNL FGV 7.8 11.5 MutS1 110e 658 IGQ MSL LGV9.7 7.0 PolB2 110f 659 IGQ LGL FGV 17.5 9.5 DnaA2 112c 660 PAQ LSLPLYL1.2 2.1 UmuC1 112d 661 EAQ LDL FDS 1.0 3.6 consensus 5-mer 112f 662   QLDL F 2.8 6.1 consensus 9-mer pep13 663 IGQ LSL FGV 4.9 5.9

[0300] These results demonstrate that the pentapeptide motifs from E.coli UmuC1, UmuC2, MutS1 and PolB2 and the hexapeptide motifs from E.coli DinB1 and DnaA2 significantly inhibit the interaction of E. coliα:β and δ:β at levels similar to that observed for the consensus 9-mer(pep13). In addition, the consensus 5-mer (112f) exhibits a similarlevel of inhibition to the consensus 9-mer (pep13). Interestingly, thetwo most inhibitory peptides, DnaA2 and UmuC1, were flanked by theirnative flanking dipeptides suggesting the flanking amino acids may makecontributions, albeit minor, to the binding ability of the peptides.

[0301] The comparable level of inhibitory activity of the pentapeptidesand hexapeptides suggests that there are at least two, and from thebioinformatics analysis, possibly several more distinct families ofβ-binding peptides. The analysis of the consensus sequence for thehexapeptides suggests that the identity of the amino acid at positionfive, whilst small amino acids are favoured, is not critical and thatthe hydrophobic amino acid at position six is likely to be equivalent tothe amino acid at position five in the pentapeptide motif.

[0302] It will be appreciated by one of skill in the art that manychanges can be made to the aspects of the invention exemplified abovewithout departing from the broad ambit and scope of the invention asdefined in the following claims.

1 678 1 25 PRT Aquifex aeolicus 1 Ser Glu Glu Glu Phe Tyr Thr Ala LeuSer Glu Thr Ser Ile Phe Gly 1 5 10 15 Gly Ser Lys Glu Lys Ala Val ValIle 20 25 2 25 PRT Thermotoga maritima 2 Lys Ile Asp Phe Ile Arg Ser LeuLeu Arg Thr Lys Thr Ile Phe Ser 1 5 10 15 Asn Lys Thr Ile Ile Asp IleVal Asn 20 25 3 22 PRT Chloroflexus aurantiacus 3 Gln Leu Val Ala AlaCys Glu Ala His Pro Phe Leu Ala Glu Arg Arg 1 5 10 15 Leu Val Ile ValTyr Asp 20 4 25 PRT Deinococcus radiodurans 4 Val Ser Ala Glu Thr LeuGly Pro His Leu Ala Pro Ser Leu Phe Gly 1 5 10 15 Asp Gly Gly Val ValVal Asp Phe Glu 20 25 5 25 PRT Porphyromonas gingivalis 5 Ser Val AlaAsp Ile Ala Asn Glu Ala Arg Arg Phe Pro Met Met Gly 1 5 10 15 Arg ArgGln Leu Ile Val Val Arg Glu 20 25 6 25 PRT Bacteroides fragilis 6 AspVal Ala Thr Val Ile Asn Ala Ala Lys Arg Tyr Pro Met Met Ser 1 5 10 15Glu His Gln Val Val Ile Val Lys Glu 20 25 7 25 PRT Cytophagahutchinsonii 7 Asn Val Ser Thr Ile Leu Gln Asn Ala Arg Lys Tyr Pro MetPhe Ser 1 5 10 15 Glu Arg Gln Val Val Met Val Lys Glu 20 25 8 25 PRTChlorobium tepidum 8 Thr Leu Gly Gln Ile Val Ser Ala Ala Ser Glu Tyr ProMet Phe Thr 1 5 10 15 Glu Lys Lys Leu Val Val Val Arg Gln 20 25 9 25 PRTChlamydia trachomatis 9 Leu Gln Gln Glu Leu Leu Ser Trp Thr Asp His PheGly Leu Phe Ala 1 5 10 15 Ser Gln Glu Thr Ile Gly Ile Tyr Gln 20 25 1025 PRT Chlamydophila pneumoniae 10 Met Pro Ala Thr Leu Met Ser Trp ThrGlu Thr Phe Ala Leu Phe Gln 1 5 10 15 Glu His Glu Thr Leu Gly Ile IleHis 20 25 11 25 PRT Nostoc punctiforme 11 Ala Ala Ile Gln Ala Leu AsnGln Val Met Thr Pro Thr Phe Gly Ala 1 5 10 15 Gly Gly Arg Leu Val TrpLeu Ile Asn 20 25 12 25 PRT Anabaena sp. 12 Ala Ala Ile Gln Ala Leu AsnGln Val Met Thr Pro Ala Phe Gly Ala 1 5 10 15 Gly Gly Arg Leu Val TrpLeu Met Asn 20 25 13 25 PRT Synechocystis sp. 13 Ala Thr Gln Arg Gly LeuGlu Gln Ala Leu Thr Pro Pro Phe Gly Ser 1 5 10 15 Gly Asp Arg Leu ValTrp Val Val Asp 20 25 14 25 PRT Prochlorococcus marinus 14 Gln Ile LysGln Ala Phe Asp Glu Ile Leu Thr Pro Pro Leu Gly Asp 1 5 10 15 Gly SerArg Val Val Val Leu Lys Asn 20 25 15 25 PRT Prochlorococcus marinus 15Gln Ala Ser Gln Ala Leu Ala Glu Ala Arg Thr Pro Pro Phe Gly Ser 1 5 1015 Gly Gly Arg Leu Val Leu Leu Gln Arg 20 25 16 25 PRT Synechococcus sp.16 Gln Ala Ala Gln Ala Leu Asp Glu Ala Arg Thr Pro Pro Phe Ala Ser 1 510 15 Gly Glu Arg Leu Val Leu Leu Gln Arg 20 25 17 25 PRT Treponemadenticola 17 Gly Met Gly Asp Val Ile Ser Leu Leu Gln Asn Ala Ser Leu PheSer 1 5 10 15 Ser Ala Lys Leu Ile Ile Leu Lys Ser 20 25 18 25 PRTTreponema pallidum 18 Pro Val Ala Asp Leu Val Asp Leu Leu Arg Thr ArgAla Leu Phe Ala 1 5 10 15 Asp Ala Val Cys Val Val Leu Tyr Asn 20 25 1925 PRT Borrelia burgdorferi 19 Ser Ala Val Gly Phe Ala Glu Lys Leu PheSer Asn Ser Phe Phe Ser 1 5 10 15 Lys Lys Glu Ile Phe Ile Val Tyr Glu 2025 20 25 PRT Magnetospirillum magnetotacticum 20 Ile Pro Ser Arg Leu AlaAsp Glu Ala Ala Ala Met Ala Leu Gly Gly 1 5 10 15 Gly Arg Arg Val ValVal Leu Arg Asp 20 25 21 25 PRT Magnetospirillum magnetotacticum 21 AspPro Gly Arg Leu Val Asp Glu Ala Gly Thr Val Gly Leu Phe Gly 1 5 10 15Gly Ser Arg Thr Ile Trp Val Arg Ser 20 25 22 25 PRT Rhodopseudomonaspalustris 22 Glu Pro Ser Arg Leu Val Asp Glu Ala Leu Ala Ile Pro Met PheGly 1 5 10 15 Gly Arg Arg Ala Ile Arg Val Arg Ala 20 25 23 25 PRTMesorhizobium loti 23 Asp Glu Gly Arg Leu Leu Asp Glu Ala Arg Thr ValPro Met Phe Ser 1 5 10 15 Asp Arg Arg Leu Leu Trp Val Arg Asn 20 25 2425 PRT Brucella suis 24 Asp Pro Ala Lys Leu Ala Asp Glu Ala Gly Thr IleSer Met Phe Gly 1 5 10 15 Gly Gln Arg Leu Ile Trp Ile Lys Asn 20 25 2525 PRT Sinorhizobium meliloti 25 Gly Ala Gly Ser Val Leu Asp Glu Val AsnAla Ile Gly Leu Phe Gly 1 5 10 15 Gly Asp Lys Leu Val Trp Val Arg Gly 2025 26 25 PRT Agrobacterium tumefaciens 26 Asp Pro Gly Arg Leu Leu AspGlu Val Asn Ala Ile Gly Leu Phe Gly 1 5 10 15 Gly Glu Lys Leu Val TrpVal Lys Ser 20 25 27 25 PRT Caulobacter crescentus 27 Asp Pro Ala LysLeu Glu Asp Glu Leu Ser Ala Met Ser Leu Met Gly 1 5 10 15 Gly Arg ArgLeu Val Arg Leu Arg Leu 20 25 28 25 PRT Rhodobacter sphaeroides 28 AspPro Ala Ala Leu Met Asp Ala Met Thr Ala Lys Gly Phe Phe Glu 1 5 10 15Gly Pro Arg Ala Val Leu Val Glu Glu 20 25 29 25 PRT Rickettsia conorii29 Asn Ile Ser Ser Leu Glu Ile Leu Leu Asn Ser Ser Asn Phe Phe Gly 1 510 15 Gln Lys Glu Leu Ile Lys Ile Arg Ser 20 25 30 25 PRT Rickettsiaprowazekii 30 Asn Ile Leu Ser Leu Asp Ile Leu Leu Asn Ser Pro Asn PhePhe Gly 1 5 10 15 Gln Lys Glu Leu Ile Lys Val Arg Ser 20 25 31 25 PRTWolbachia sp. 31 Ser Pro Ser Leu Leu Phe Ser Glu Leu Ala Asn Val Ser MetPhe Thr 1 5 10 15 Ser Lys Lys Leu Ile Lys Leu Ile Asn 20 25 32 25 PRTNeisseria gonorrhoeae 32 Asp Trp Asn Glu Leu Leu Gln Thr Ala Gly Asn AlaGly Leu Phe Ala 1 5 10 15 Asp Leu Lys Leu Leu Glu Leu His Ile 20 25 3325 PRT Neisseria meningitidis 33 Asp Trp Asn Glu Leu Leu Gln Thr Ala GlySer Ala Gly Leu Phe Ala 1 5 10 15 Asp Leu Lys Leu Leu Glu Leu His Ile 2025 34 25 PRT Nitrosomonas europaea 34 Asp Trp Met Asn Leu Phe Gln TrpGly Arg Gln Ser Ser Leu Phe Ser 1 5 10 15 Glu Arg Arg Met Leu Asp LeuArg Ile 20 25 35 25 PRT Bordetella pertussis 35 Asp Trp Ser Ala Val AlaAla Ala Thr Gln Ser Val Ser Leu Phe Gly 1 5 10 15 Asp Arg Arg Leu LeuGlu Leu Lys Ile 20 25 36 25 PRT Burkholderia pseudomallei 36 Asp Trp SerThr Leu Ile Gly Ala Ser Gln Ala Met Ser Leu Phe Gly 1 5 10 15 Glu ArgGln Leu Val Glu Leu Arg Ile 20 25 37 25 PRT Burkholderia cepacia 37 AspTrp Ser Ser Leu Leu Gly Ala Ser Gln Ser Met Ser Leu Phe Gly 1 5 10 15Asp Arg Gln Leu Val Glu Leu Arg Ile 20 25 38 25 PRT Burkholderia mallei38 Asp Trp Ser Thr Leu Ile Gly Ala Ser Gln Ala Met Ser Leu Phe Gly 1 510 15 Glu Arg Gln Leu Val Glu Leu Arg Ile 20 25 39 25 PRT Ralstoniametallidurans 39 Gln Trp Gly Gln Val Ile Glu Ala Gln Gln Ser Met Ser LeuPhe Gly 1 5 10 15 Asp Arg Lys Ile Val Glu Leu Arg Ile 20 25 40 25 PRTAcidothiobacillus ferrooxidans 40 Ile Trp Asp Ala Leu Arg Asp Glu ArgAsp Ala Gly Ser Leu Phe Ala 1 5 10 15 Ala Gln Arg Val Leu Leu Leu ArgLeu 20 25 41 25 PRT Xylella fastidiosa 41 Asp Trp Gln Gln Leu Ala SerSer Phe Asn Ala Pro Ser Leu Phe Ser 1 5 10 15 Ser Arg Arg Leu Ile GluIle Arg Leu 20 25 42 25 PRT Legionella pneumophila 42 Glu Trp His ValVal Leu Glu Glu Thr Asn Asn Tyr Ser Leu Phe Tyr 1 5 10 15 Gln Thr ValIle Leu Thr Ile Phe Phe 20 25 43 25 PRT Coxiella burnetii 43 His Trp GlnSer Leu Thr Gln Ser Phe Asp Asn Phe Ser Leu Leu Ser 1 5 10 15 Asp LysThr Leu Ile Glu Leu Arg Asn 20 25 44 25 PRT Methylococcus capsulatus 44Ser Trp Ser Thr Phe Leu Glu Ala Gly Asp Ser Val Pro Leu Phe Gly 1 5 1015 Asp Arg Arg Ile Leu Asp Leu Arg Leu 20 25 45 25 PRT Pseudomonasaeruginosa 45 Asp Trp Gly Leu Leu Leu Glu Ala Gly Ala Ser Leu Ser LeuPhe Ala 1 5 10 15 Glu Lys Arg Leu Ile Glu Leu Arg Leu 20 25 46 25 PRTPseudomonas putida 46 Asp Trp Gly Thr Leu Leu Gln Ala Gly Ala Ser LeuSer Leu Phe Ala 1 5 10 15 Gln Arg Arg Leu Leu Glu Leu Arg Leu 20 25 4725 PRT Pseudomonas syringae 47 Asp Trp Gly Thr Leu Leu Gln Ala Gly AlaSer Met Ser Leu Phe Ala 1 5 10 15 Glu Arg Arg Leu Leu Glu Leu Arg Leu 2025 48 25 PRT Pseudomonas fluorescens 48 Asp Trp Gly Thr Leu Leu Gln AlaGly Ala Ser Met Ser Leu Phe Ala 1 5 10 15 Glu Lys Arg Leu Leu Glu LeuArg Leu 20 25 49 25 PRT Shewanella putrefaciens 49 Asn Trp Gly Asp LeuThr Gln Glu Trp Gln Ala Met Ser Leu Phe Ser 1 5 10 15 Ser Arg Arg IleIle Glu Leu Thr Leu 20 25 50 25 PRT Vibrio cholerae 50 Asp Trp Asn AlaVal Tyr Asp Cys Cys Gln Ala Leu Ser Leu Phe Ser 1 5 10 15 Ser Arg GlnLeu Ile Glu Ile Glu Ile 20 25 51 25 PRT Pasteurella multocida 51 Asn TrpSer Asp Leu Phe Glu Arg Cys Gln Ser Ile Gly Leu Phe Phe 1 5 10 15 AsnLys Gln Ile Leu Phe Leu Asn Leu 20 25 52 25 PRT Haemophilus influenzae52 Asp Trp Ala Gln Leu Ile Glu Ser Cys Gln Ser Ile Gly Leu Phe Phe 1 510 15 Ser Lys Gln Ile Leu Ser Leu Asn Leu 20 25 53 25 PRT Haemophilusducreyi 53 Lys Trp Glu Gln Leu Phe Glu Ser Val Gln Asn Phe Gly Leu PhePhe 1 5 10 15 Ser Arg Gln Ile Ile Ile Leu Asn Leu 20 25 54 25 PRTActinobacillus actinomycetemcomitans 54 Asp Trp Asn Asp Leu Phe Glu ArgVal Gln Ser Met Gly Leu Phe Phe 1 5 10 15 Asn Lys Gln Leu Ile Ile LeuAsp Leu 20 25 55 25 PRT Buchnera sp. 55 Asp Trp Lys Lys Ile Ile Leu PheTyr Lys Thr Asn Asn Leu Phe Phe 1 5 10 15 Lys Lys Thr Thr Leu Val IleAsn Phe 20 25 56 25 PRT Escherichia coli 56 Asp Trp Asn Ala Ile Phe SerLeu Cys Gln Ala Met Ser Leu Phe Ala 1 5 10 15 Ser Arg Gln Thr Leu LeuLeu Leu Leu 20 25 57 25 PRT Salmonella typhi 57 Asp Trp Gly Ser Leu PheSer Leu Cys Gln Ala Met Ser Leu Phe Ala 1 5 10 15 Ser Arg Gln Thr LeuVal Leu Gln Leu 20 25 58 25 PRT Salmonella typhimurium 58 Asp Trp GlySer Leu Phe Ser Leu Cys Gln Ala Met Ser Leu Phe Ala 1 5 10 15 Ser ArgGln Thr Leu Val Leu Gln Leu 20 25 59 25 PRT Klebsiella pneumoniae 59 ProThr Gly Arg Arg Phe Ser Leu Lys Pro Gly Asp Glu Leu Phe Ala 1 5 10 15Ser Arg Gln Thr Leu Leu Leu Ile Leu 20 25 60 25 PRT Yersinia pestis 60Glu Trp Glu His Ile Phe Ser Leu Cys Gln Ala Leu Ser Leu Phe Ala 1 5 1015 Ser Arg Gln Thr Leu Leu Leu Ser Phe 20 25 61 25 PRT Yersiniapseudotuberculosis 61 Glu Trp Glu His Ile Phe Ser Leu Cys Gln Ala LeuSer Leu Phe Ala 1 5 10 15 Ser Arg Gln Thr Leu Leu Leu Ser Phe 20 25 6225 PRT Desulfovibrio vulgaris 62 Leu Pro Pro Val Phe Trp Glu His Leu ThrLeu Gln Gly Leu Phe Gly 1 5 10 15 Ser Pro Arg Ala Leu Val Val Arg Asn 2025 63 25 PRT Geobacter sulfurreducens 63 Lys Gly Asp Asp Ile Ala Thr AlaAla Gln Thr Leu Pro Met Phe Ala 1 5 10 15 Asp Arg Arg Met Val Leu ValLys Arg 20 25 64 25 PRT Helicobacter pylori 64 Glu Lys Ser Gln Ile AlaThr Leu Leu Glu Gln Asp Ser Leu Phe Gly 1 5 10 15 Gly Ser Ser Leu ValIle Leu Lys Leu 20 25 65 25 PRT Campylobacter jejuni 65 Asn Phe Thr ArgAla Ser Asp Phe Leu Ser Ala Gly Ser Leu Phe Ser 1 5 10 15 Glu Lys LysLeu Leu Glu Ile Lys Thr 20 25 66 25 PRT Streptomyces coelicolor 66 LeuGln Pro Gly Thr Leu Ala Glu Leu Thr Ser Pro Ser Leu Phe Ala 1 5 10 15Glu Arg Lys Val Val Val Val Arg Asn 20 25 67 25 PRT Thermobifida fusca67 Val Ser Ala Gly Lys Leu Val Glu Val Thr Ser Pro Ser Leu Phe Gly 1 510 15 Asp Arg Arg Val Val Val Leu Arg Ser 20 25 68 25 PRT Mycobacteriumavium 68 Val Ser Thr Tyr Glu Leu Ala Glu Leu Leu Ser Pro Ser Leu Phe Ala1 5 10 15 Glu Glu Arg Ile Val Val Leu Glu Ala 20 25 69 25 PRTMycobacterium leprae 69 Val Gly Thr Tyr Glu Leu Thr Glu Leu Leu Ser ProSer Leu Phe Ala 1 5 10 15 Asp Glu Arg Ile Val Val Leu Glu Ala 20 25 7025 PRT Mycobacterium smegmatis 70 Val Ser Thr Ser Glu Leu Ala Glu LeuLeu Ser Pro Ser Leu Phe Ala 1 5 10 15 Glu Glu Arg Leu Val Val Leu GluAla 20 25 71 25 PRT Mycobacterium tuberculosis 71 Val Gly Ala Tyr GluLeu Ala Glu Leu Leu Ser Pro Ser Leu Phe Ala 1 5 10 15 Glu Glu Arg IleVal Val Leu Gly Ala 20 25 72 25 PRT Corynebacterium diptheriae 72 ValAsn Ala Ser Glu Leu Ile Gln Leu Thr Ser Pro Ser Leu Phe Gly 1 5 10 15Glu Asp Arg Ile Ile Val Leu Thr Asn 20 25 73 25 PRT Dehalococcoidesethenogenes 73 Thr Ala Ala Glu Leu Gln Asn Tyr Val Gln Thr Ile Pro PheLeu Ala 1 5 10 15 Pro Ala Arg Leu Val Met Val Asn Gly 20 25 74 20 PRTClostridium difficile 74 Val Leu Asn His Leu Ile Ser Ser Ile Glu Thr LeuPro Phe Met Asp 1 5 10 15 Asp Arg Lys Ile 20 75 25 PRT Carboxydothermushydrogenoformans 75 Leu Pro Glu Glu Val Val Ala Arg Ala Glu Thr Val SerPhe Phe Gly 1 5 10 15 Gln Arg Phe Ile Val Val Lys Asn Cys 20 25 76 25PRT Bacillus halodurans 76 Pro Ile Glu Ala Ala Leu Glu Glu Ala Glu ThrVal Pro Phe Phe Gly 1 5 10 15 Ser Lys Arg Val Val Ile Leu Lys Asp 20 2577 25 PRT Bacillus stearothermophilus 77 Pro Ile Glu Ala Ala Leu Glu GluAla Glu Thr Val Pro Phe Phe Gly 1 5 10 15 Glu Arg Arg Val Ile Leu IleLys His 20 25 78 25 PRT Bacillus subtilis 78 Pro Leu Asp Gln Ala Ile AlaAsp Ala Glu Thr Phe Pro Phe Met Gly 1 5 10 15 Glu Arg Arg Leu Val IleVal Lys Asn 20 25 79 25 PRT Staphylococcus aureus 79 Glu Ile Ala Pro IleVal Glu Glu Thr Leu Thr Leu Pro Phe Phe Ser 1 5 10 15 Asp Lys Lys AlaIle Leu Val Lys Asn 20 25 80 25 PRT Staphylococcus epidermidis 80 AspLeu Thr Pro Ile Ile Glu Glu Thr Leu Thr Met Pro Phe Phe Ser 1 5 10 15Asn Lys Lys Ala Ile Val Val Lys Asn 20 25 81 25 PRT Bacillus anthracis81 Tyr Leu Glu Asp Val Val Glu Asp Ala Arg Thr Leu Pro Phe Phe Gly 1 510 15 Glu Arg Lys Val Leu Leu Ile Lys Ser 20 25 82 25 PRT Listeriainnocua 82 Pro Ile Glu Val Val Ile Gln Glu Ala Glu Ser Met Pro Phe PheGly 1 5 10 15 Asp Lys Arg Leu Val Met Ala Asn Asn 20 25 83 25 PRTListeria monocytogenes 83 Pro Ile Glu Val Val Ile Gln Glu Ala Glu SerMet Pro Phe Phe Gly 1 5 10 15 Asp Lys Arg Leu Val Met Ala Asn Asn 20 2584 25 PRT Listeria monocytogenes 84 Pro Ile Glu Val Val Val Gln Glu AlaGlu Ser Met Pro Phe Phe Gly 1 5 10 15 Asp Lys Arg Leu Val Met Ala AsnAsn 20 25 85 25 PRT Enterococcus faecalis 85 Pro Leu Ser Ala Ala Ile AlaGlu Ala Glu Thr Ile Pro Phe Phe Gly 1 5 10 15 Asp Tyr Arg Leu Val PheVal Glu Asn 20 25 86 25 PRT Enterococcus faecium 86 Ser Leu Asp Glu ValVal Ala Glu Ala Glu Thr Leu Pro Phe Phe Gly 1 5 10 15 Asp Gln Arg LeuVal Phe Val Glu Asn 20 25 87 25 PRT Lactococcus lactis 87 Asn Ser AspLeu Ala Leu Glu Asp Leu Glu Ser Leu Pro Phe Phe Ser 1 5 10 15 Asp SerArg Leu Val Ile Leu Glu Asn 20 25 88 25 PRT Streptococcus equi 88 LeuTyr Gln Thr Ala Glu Met Asp Leu Val Ser Met Pro Phe Phe Ala 1 5 10 15Asp Gln Lys Val Val Ile Phe Asp His 20 25 89 25 PRT Streptococcusagalactiae 89 Asp Tyr Gln Asn Ala Glu Leu Asp Leu Glu Ser Leu Pro PheLeu Ser 1 5 10 15 Asp Tyr Lys Val Val Ile Phe Asp Gln 20 25 90 25 PRTStreptococcus pyogenes 90 Ala Tyr Gln Asp Ala Glu Met Asp Leu Val SerLeu Pro Phe Phe Ala 1 5 10 15 Glu Gln Lys Val Val Ile Phe Asp His 20 2591 25 PRT Streptococcus mutans 91 Ser Tyr Gln Asp Ala Glu Met Asp LeuGlu Ser Leu Pro Phe Phe Ala 1 5 10 15 Asp Glu Lys Ile Val Ile Phe AspAsn 20 25 92 25 PRT Streptococcus gordonii 92 Asp Tyr Gln Gln Val GluLeu Asp Leu Val Ser Leu Pro Phe Phe Ser 1 5 10 15 Asp Glu Lys Ile IleIle Leu Asp His 20 25 93 25 PRT Streptococcus pneumoniae 93 Val Tyr LysAsp Val Glu Leu Glu Leu Val Ser Leu Pro Phe Phe Ala 1 5 10 15 Asp GluLys Ile Val Ile Leu Asp Tyr 20 25 94 25 PRT Ureaplasma urealyticum 94Ser Leu Ile Ser Phe Lys Asn Leu Ile Glu Gln Asp Asp Leu Phe Asn 1 5 1015 Ser Asn Lys Ile Tyr Leu Phe Lys Asn 20 25 95 25 PRT Mycoplasmagenitalium 95 Lys Asp Leu Lys Gln Leu Tyr Asp Leu Phe Ser Gln Pro LeuPhe Gly 1 5 10 15 Ser Asn Asn Glu Lys Phe Ile Val Asn 20 25 96 25 PRTMycoplasma pneumoniae 96 Asp Val Asn Lys Leu Tyr Asp Val Val Leu Asn GlnAsn Leu Phe Ala 1 5 10 15 Glu Asp Thr Lys Pro Ile Leu Ile His 20 25 9725 PRT Mycoplasma pulmonis 97 Glu Ile Asp Asp Leu Leu Asn Asp Ile ValGln Lys Asp Leu Phe Ser 1 5 10 15 Pro Asn Lys Ile Ile His Ile Lys Asn 2025 98 25 PRT Clostridium acetobutylicum 98 Glu Phe Glu Asp Ile Leu AsnAla Cys Glu Thr Val Pro Phe Met Ser 1 5 10 15 Glu Lys Arg Met Val ValVal Tyr Arg 20 25 99 15 PRT Magnetococcus sp. 99 Ser Ser Gln Thr Ala ThrThr Gln Pro Gln Gln Leu Ser Leu Phe 1 5 10 15 100 25 PRT Cytophagahutchinsonii 100 Lys Leu Ser Asn Leu Val His Gly Asn Tyr Gln Ile Ser LeuPhe Glu 1 5 10 15 Asp Ser Glu Lys Asn Gln Asn Leu Tyr 20 25 101 25 PRTTreponema denticola 101 Met Asn Ile Glu Ser Asp Ile Pro Glu Ala Gln ThrGlu Leu Phe Tyr 1 5 10 15 Ser Glu Lys Asn Val Lys Lys Arg Lys 20 25 10220 PRT Magnetospirillum magnetotacticum 102 Thr Asp Leu Cys Pro Ala GluAsp Ala Asp Pro Pro Asp Leu Phe Gly 1 5 10 15 Pro Arg Pro Ala 20 103 25PRT Magnetospirillum magnetotacticum 103 Leu Gly Glu Leu Ser Arg Thr GluArg Arg Gln Leu Asp Leu Leu Thr 1 5 10 15 Asn Asp Glu Pro Val Arg LysArg Leu 20 25 104 25 PRT Methylobacterium extorquens 104 Gly Asp Leu CysGly Ala Ile His Ala Asp Arg Gly Asp Leu Ala Asp 1 5 10 15 Gln Gly IleGlu Arg Val Ala Arg Arg 20 25 105 25 PRT Rhodopseudomonas palustris 105Ser Ala Leu Thr Glu Gln Thr Gly Pro Ala Glu Asp Asp Met Leu Asp 1 5 1015 Arg Arg Ser Ala His Ala Glu Arg Ala 20 25 106 16 PRT Mesorhizobiumloti 106 Leu Gly Asp Val Leu Pro Pro Asp Gln Arg Gln Leu Arg Phe Glu Leu1 5 10 15 107 25 PRT Mesorhizobium loti 107 Ser Asp Leu Ser Asp Asp AspLys Ala Asp Pro Pro Asp Leu Val Asp 1 5 10 15 Val Gln Ser Arg Lys ArgAla Met Ala 20 25 108 26 PRT Mesorhizobium loti 108 Val Ser His Leu GluGlu Ser Ala Glu Leu Gln Leu Asp Leu Pro Leu 1 5 10 15 Gly Leu Ala AspGlu Lys Arg Arg Pro Gly 20 25 109 25 PRT Brucella suis 109 Ser Asp LeuSer Pro Ser Asp Arg Ala Asp Pro Pro Asp Leu Val Asp 1 5 10 15 Ile GlnAla Thr Lys Arg Ala Val Ala 20 25 110 25 PRT Sinorhizobium meliloti 110Ser Asp Leu Val Asp Pro Asp Leu Ala Asp Pro Pro Asp Leu Val Asp 1 5 1015 Pro Gln Ala Ser Arg Arg Ala Ala Ala 20 25 111 16 PRT Sinorhizobiummeliloti 111 Leu Asp Thr Val Asp Asp Arg Ser Glu Pro Gln Leu Ala Leu AlaLeu 1 5 10 15 112 25 PRT Agrobacterium tumefaciens 112 Ser Asp Leu ArgAsp Ala Gly Leu Ala Asp Pro Pro Asp Leu Val Asp 1 5 10 15 Arg Gln AlaThr Arg Arg Ala Ala Ala 20 25 113 16 PRT Agrobacterium tumefaciens 113Asp Gln Glu Ala Glu Asp Glu Glu Gln Pro Gln Leu Asp Leu Ala Leu 1 5 1015 114 25 PRT Caulobacter crescentus 114 Leu Thr Glu Phe Val Asp Ala AspThr Ala Gly Ala Asp Met Phe Ala 1 5 10 15 Asp Glu Glu Arg Arg Ala LeuLys Ser 20 25 115 25 PRT Rhodobacter sphaeroides 115 Ala Gly Ala Ala GluAla Asp Leu Thr Gly Thr Gly Asp Leu Leu Asp 1 5 10 15 Pro Asn Ala GlyArg Arg Ile Ala Ala 20 25 116 25 PRT Rhodobacter capsulatus 116 Asp LeuSer Pro Ala Gly Gly Arg Asp Pro Ile Gly Asp Leu Leu Asp 1 5 10 15 ProGln Ala Thr Ala Arg Ala Ala Ala 20 25 117 16 PRT Sphingomonasaromaticivorans 117 Ala Glu Asp Gly Pro Ser Gly Ala Ala Leu Gln Ala GluLeu Pro Phe 1 5 10 15 118 16 PRT Neisseria gonorrhoeae 118 Gly Val GlyArg Leu Val Pro Lys Asn Gln Gln Gln Asp Leu Trp Ala 1 5 10 15 119 16 PRTNeisseria meningitidis 119 Gly Val Gly His Leu Val Pro Lys Asn Gln GlnGln Asp Leu Trp Ala 1 5 10 15 120 15 PRT Nitrosomonas europaea 120 SerAla Leu Leu Lys Glu Asn Tyr Tyr Phe Gln Glu Glu Leu Phe 1 5 10 15 121 19PRT Bordetella pertussis 121 Phe Pro Asp Ala Gln Ala Glu Ala Pro Arg GlnAla Glu Leu Phe Gly 1 5 10 15 Asp Ala Phe 122 15 PRT Burkholderiapseudomallei 122 Ile Asp Glu Asp Thr Ala Glu Arg His Gly Gln Ile Ala LeuPhe 1 5 10 15 123 20 PRT Burkholderia cepacia 123 Ala Leu Thr Pro ProArg Arg Leu Pro Val Gln Ala Asp Leu Pro Phe 1 5 10 15 Ala Ser Asp Glu 20124 25 PRT Burkholderia mallei 124 Ile Asp Glu Asp Thr Ala Glu Arg HisGly Gln Ile Ala Leu Phe Asp 1 5 10 15 Asp Glu Asp Met Ser Asp Glu AspAla 20 25 125 26 PRT Ralstonia metallidurans 125 Ala Asp Gln Gly Asp AspPro Ala Pro Val Gln Glu Glu Leu Arg Phe 1 5 10 15 Asp Ala Glu Pro AspSer Pro Val Phe Arg 20 25 126 22 PRT Acidothiobacillus ferrooxidans 126Asn Val Glu Ala Val Pro Pro Glu Ala Leu Gln Met Asn Leu Leu Glu 1 5 1015 Glu Pro Val Asp Leu Arg 20 127 17 PRT Legionella pneumophila 127 LeuLys Gln Glu Asn Thr Tyr Gln Ser Val Gln Leu Pro Leu Leu Asp 1 5 10 15Leu 128 16 PRT Coxiella burnetii 128 Ser Phe Ser Glu Asp Pro Leu Leu GluLeu Gln Arg Thr Phe Glu Trp 1 5 10 15 129 15 PRT Pseudomonas aeruginosa129 Arg Leu Leu Asp Leu Gln Gly Ala His Glu Gln Leu Arg Leu Phe 1 5 1015 130 18 PRT Pseudomonas putida 130 Arg Leu Arg Asp Leu Arg Gly Ala HisGlu Gln Leu Glu Leu Phe Pro 1 5 10 15 Pro Lys 131 17 PRT Pseudomonassyringae 131 Arg Leu His Asp Leu Arg Asp Ala His Glu Gln Leu Glu Leu PheSer 1 5 10 15 Thr 132 17 PRT Pseudomonas fluorescens 132 Arg Leu Glu AspLeu Arg Gly Gly Phe Glu Gln Met Glu Leu Phe Glu 1 5 10 15 Arg 133 16 PRTShewanella putrefaciens 133 Leu Ile Ser Glu Val Asp Pro Leu Gln Thr GlnLeu Val Leu Ser Ile 1 5 10 15 134 21 PRT Vibrio cholerae 134 Val Met LeuLys Pro Glu Leu Gln Met Lys Gln Leu Ser Met Phe Pro 1 5 10 15 Ser AspGly Trp Gln 20 135 15 PRT Pasteurella multocida 135 Pro Glu Thr Thr GluSer Lys Thr Gln Val Gln Met Ser Leu Trp 1 5 10 15 136 15 PRT Haemophilusinfluenzae 136 Val Asn Leu Pro Glu Glu Asn Lys Gln Glu Gln Met Ser LeuTrp 1 5 10 15 137 15 PRT Actinobacillus actinomycetemcomitans 137 ValThr Leu Pro Glu Glu Lys Gln Ser Glu Gln Met Ser Leu Trp 1 5 10 15 138 16PRT Escherichia coli 138 Val Thr Leu Leu Asp Pro Gln Met Glu Arg Gln LeuVal Leu Gly Leu 1 5 10 15 139 16 PRT Salmonella typhi 139 Val Thr LeuLeu Asp Pro Gln Leu Glu Arg Gln Leu Val Leu Gly Leu 1 5 10 15 140 16 PRTSalmonella typhimurium 140 Val Thr Leu Leu Asp Pro Gln Leu Glu Arg GlnLeu Val Leu Gly Leu 1 5 10 15 141 16 PRT Klebsiella pneumoniae 141 ValThr Leu Leu Asp Pro Gln Leu Glu Arg Gln Leu Leu Leu Gly Ile 1 5 10 15142 17 PRT Yersinia pestis 142 Val Thr Leu Leu Asp Pro Gln Leu Glu ArgGln Leu Leu Leu Asp Trp 1 5 10 15 Gly 143 26 PRT Desulfovibrio vulgaris143 Leu Gly Val Ser His Phe Gly Gly Glu Arg Gln Met Ser Leu Pro Ile 1 510 15 Gly Gly Met Pro Arg Arg Asp Asp Thr Arg 20 25 144 25 PRT Geobactersulfurreducens 144 Ala Ile Ser Asn Leu Val His Ala Ser Glu Gln Leu ProLeu Phe Pro 1 5 10 15 Glu Glu Arg Arg Leu Thr Thr Leu Ser 20 25 145 25PRT Geobacter sulfurreducens 145 Arg Ile Thr Asn Leu Cys Tyr Gln Arg GluGln Leu Pro Leu Phe Glu 1 5 10 15 Lys Glu Arg Arg Lys Ala Leu Ala Thr 2025 146 26 PRT Streptomyces coelicolor 146 Ser Leu Thr Ser Ala Glu HisAla Ser His Gln Leu Thr Phe Asp Pro 1 5 10 15 Val Asp Glu Lys Val ArgArg Ile Glu Glu 20 25 147 25 PRT Thermobifida fusca 147 Gly Leu Val SerAla Asp Arg Val His His Gln Leu Ala Leu Asp Glu 1 5 10 15 Glu Gly ProGly Trp Arg Ala Val Glu 20 25 148 26 PRT Mycobacterium avium 148 Val SerGly Ile Asp Arg Asp Gly Ala Gln Gln Leu Met Leu Pro Phe 1 5 10 15 GluGly Arg Pro Pro Asp Ala Ile Asp Ala 20 25 149 25 PRT Mycobacterium avium149 Val Gly Phe Ser Gly Leu Ser Glu Val Arg Gln Glu Ser Leu Phe Pro 1 510 15 Asp Leu Glu Met Pro Ala Pro Gln Ser 20 25 150 26 PRT Mycobacteriumsmegmatis 150 Val Ser Asn Ile Asp Arg Gly Gly Thr Gln Gln Leu Glu LeuPro Phe 1 5 10 15 Ala Glu Gln Pro Asp Pro Val Ala Ile Asp 20 25 151 25PRT Mycobacterium smegmatis 151 Val Gly Phe Ser Gly Leu Ser Asp Ile ArgGln Glu Ser Leu Phe Pro 1 5 10 15 Asp Leu Glu Gln Pro Glu Glu Phe Pro 2025 152 25 PRT Mycobacterium tuberculosis 152 Val Gly Phe Ser Gly Leu SerAsp Ile Arg Gln Glu Ser Leu Phe Ala 1 5 10 15 Asp Ser Asp Leu Thr GlnGlu Thr Ala 20 25 153 25 PRT Corynebacterium diptheriae 153 Val Gly LeuSer Gly Leu Glu Asp Ala Arg Gln Asp Ile Leu Phe Pro 1 5 10 15 Glu LeuAsp Arg Val Val Pro Val Lys 20 25 154 26 PRT Dehalococcoides ethenogenes154 Gly Ile Ser Asp Phe Cys Gly Pro Glu Lys Gln Leu Glu Ile Asp Pro 1 510 15 Ala Arg Ala Arg Leu Glu Lys Leu Asp Ala 20 25 155 25 PRTDesulfitobacterium hafniense 155 Thr Ala Ser Arg Leu Gln Lys Gly Ile GluGln Leu Ser Leu Phe Gln 1 5 10 15 Glu Glu Ser Glu Glu Gln Thr Glu Leu 2025 156 23 PRT Clostridium difficile 156 Asn Leu Ser Asp Lys Lys Glu ThrTyr Lys Asp Ile Thr Leu Phe Glu 1 5 10 15 Tyr Met Asp Ser Ile Gln Met 20157 25 PRT Carboxydothermus hydrogenoformans 157 Thr Pro Leu Val Pro ValGly Gly Gly Arg Gln Ile Ser Leu Phe Gly 1 5 10 15 Glu Asp Leu Arg ArgGlu Asn Leu Tyr 20 25 158 25 PRT Bacillus halodurans 158 Asp Val Ile AspLys Lys Tyr Ala Tyr Glu Pro Leu Asp Leu Phe Arg 1 5 10 15 Tyr Glu GluGln Ile Lys Gln Ala Thr 20 25 159 25 PRT Bacillus stearothermophilus 159His Val Phe Asp Glu Arg Glu Glu Gly Lys Gln Leu Asp Leu Phe Arg 1 5 1015 Tyr Glu Glu Glu Ala Lys Val Glu Glu 20 25 160 25 PRT Bacillussubtilis 160 Asp Leu Val Glu Lys Glu Gln Ala Tyr Lys Gln Leu Asp Leu PheSer 1 5 10 15 Phe Asn Glu Asp Ala Lys Asp Glu Pro 20 25 161 18 PRTStaphylococcus aureus 161 Val Gly Asn Leu Glu Gln Ser Thr Tyr Lys AsnMet Thr Ile Tyr Asp 1 5 10 15 Phe Ile 162 18 PRT Staphylococcusepidermidis 162 Val Gly Ser Leu Glu Gln Ser Asp Phe Lys Asn Leu Thr IleTyr Asp 1 5 10 15 Phe Ile 163 25 PRT Bacillus anthracis 163 Glu Ile GluTrp Lys Thr Glu Ser Val Lys Gln Leu Asp Leu Phe Ser 1 5 10 15 Phe GluGlu Asp Ala Lys Glu Glu Pro 20 25 164 17 PRT Listeria innocua 164 ValThr Asn Leu Lys Pro Val Tyr Phe Glu Asn Leu Arg Leu Glu Gly 1 5 10 15Leu 165 17 PRT Listeria monocytogenes 165 Val Thr Asn Leu Lys Pro ValTyr Phe Glu Asn Leu Arg Leu Glu Gly 1 5 10 15 Leu 166 17 PRT Listeriamonocytogenes 166 Val Thr Asn Leu Lys Pro Val Tyr Phe Glu Asn Leu ArgLeu Glu Gly 1 5 10 15 Leu 167 18 PRT Enterococcus faecalis 167 Asn LeuAsp Pro Leu Ala Tyr Glu Asn Ile Val Leu Pro Leu Trp Glu 1 5 10 15 LysSer 168 20 PRT Enterococcus faecium 168 Asn Leu Asp Pro Met Thr Tyr GluAsn Ile Val Leu Pro Leu Trp Glu 1 5 10 15 Asn Gln Glu Ile 20 169 17 PRTLactococcus lactis 169 Gly Val Thr Val Thr Glu Phe Gly Ala Gln Lys AlaThr Leu Asp Met 1 5 10 15 Gln 170 19 PRT Streptococcus equi 170 Thr MetThr Gly Leu Lys Asp Lys Val Thr Asp Ile Leu Leu Asp Leu 1 5 10 15 SerPhe Asn 171 16 PRT Streptococcus pyogenes 171 Thr Met Thr Met Leu GluAsp Lys Val Ala Asp Ile Ser Leu Asp Leu 1 5 10 15 172 21 PRTStreptococcus mutans 172 Val Thr Ala Leu Glu Asp Ser Thr Arg Glu Glu LeuSer Leu Thr Ala 1 5 10 15 Asp Asp Phe Lys Thr 20 173 16 PRT Ureaplasmaurealyticum 173 Lys Leu Val Lys Lys Glu Asn Val Lys Lys Gln Leu Phe LeuPhe Asp 1 5 10 15 174 25 PRT Mycoplasma genitalium 174 Leu Lys Lys IleAsp Thr Asp Glu Gly Gln Lys Lys Ser Leu Phe Tyr 1 5 10 15 Gln Phe IlePro Lys Ser Ile Ser Lys 20 25 175 25 PRT Mycoplasma pneumoniae 175 LeuLys Asn Asn Pro Ser Ser Ser Arg Pro Glu Gly Leu Leu Phe Tyr 1 5 10 15Glu Tyr Gln Gln Ala Lys Pro Lys Gln 20 25 176 25 PRT Mycoplasma pulmonis176 Asp Phe Gly Asp Ile Tyr Gln Ser Asp Leu Ser Phe Asp Leu Phe Asp 1 510 15 Gln Lys Tyr Asp Ser Lys Lys Glu Lys 20 25 177 25 PRT Clostridiumacetobutylicum 177 Leu Ser Gly Leu Cys Ser Gly Ser Ser Val Gln Ile SerMet Phe Asp 1 5 10 15 Glu Lys Thr Asp Thr Arg Asn Glu Ile 20 25 178 25PRT Fibrobacter succinogenes 178 Ala Asn Asn Val Leu Glu Ala Thr Gln GluSer Tyr Asp Leu Phe Thr 1 5 10 15 Asp Val Lys Lys Ile Glu Arg Glu Lys 2025 179 25 PRT Bacillus halodurans 179 Leu Ser Asn Leu Thr Ser Asp GluAla Trp Gln Leu Ser Phe Phe Gly 1 5 10 15 Asn Arg Asp Arg Ala His GlnLeu Gly 20 25 180 25 PRT Bacillus subtilis 180 Leu Ser Asn Ile Glu AspAsp Val Asn Gln Gln Leu Ser Leu Phe Glu 1 5 10 15 Val Asp Asn Glu LysArg Arg Lys Leu 20 25 181 25 PRT Bacillus subtilis 181 Leu Ser Gln LeuSer Ser Asp Asp Ile Trp Gln Leu Asn Leu Phe Gln 1 5 10 15 Asp Tyr AlaLys Lys Met Ser Leu Gly 20 25 182 25 PRT Staphylococcus aureus 182 LeuSer Gln Phe Ile Asn Glu Asp Glu Arg Gln Leu Ser Leu Phe Glu 1 5 10 15Asp Glu Tyr Gln Arg Lys Arg Asp Glu 20 25 183 25 PRT Staphylococcusepidermidis 183 Leu Thr Gln Phe Ile Lys Glu Ser Asp Arg Gln Leu Asn LeuPhe Ile 1 5 10 15 Asp Glu Tyr Glu Arg Lys Lys Asp Val 20 25 184 25 PRTBacillus anthracis 184 Leu Thr Asn Leu Leu Gln Glu Gly Glu Glu Gln IleSer Leu Phe Asp 1 5 10 15 Asn Val Thr Gln Arg Glu Gln Glu Val 20 25 18525 PRT Bacillus anthracis 185 Leu Thr Lys Leu Ile Gly Glu Gly Glu GluGln Ile Ser Leu Phe Asp 1 5 10 15 Asn Ile Ile Gln Arg Glu Lys Glu Ile 2025 186 25 PRT Listeria innocua 186 Cys Gly Lys Leu Thr Leu Lys Thr GlyLeu Gln Leu Asn Leu Phe Glu 1 5 10 15 Asp Ala Thr Arg Thr Leu Asn HisGlu 20 25 187 25 PRT Listeria innocua 187 Cys Ala Gly Ile Lys Arg LysThr Ser Met Gln Leu Ser Val Phe Glu 1 5 10 15 Asp Tyr Thr Lys Thr LeuGln Gln Glu 20 25 188 25 PRT Listeria monocytogenes 188 Cys Gly Lys IleThr Leu Lys Thr Gly Leu Gln Leu Asn Leu Phe Glu 1 5 10 15 Asp Ala ThrArg Thr Leu Asn His Glu 20 25 189 25 PRT Listeria monocytogenes 189 CysGly Lys Ile Thr Leu Lys Thr Gly Leu Gln Leu Asn Leu Phe Glu 1 5 10 15Asp Phe Thr Gln Thr Leu Asn His Glu 20 25 190 25 PRT Enterococcusfaecalis 190 Tyr Gly Arg Leu Val Trp Asn Lys Asn Leu Gln Leu Asp Leu PhePro 1 5 10 15 Val Pro Glu Glu Gln Ile His Glu Thr 20 25 191 25 PRTEnterococcus faecalis 191 Tyr Gly Lys Leu Val Trp Asn Glu Ser Leu GlnLeu Asp Leu Phe Ser 1 5 10 15 Glu Pro Glu Glu Gln Ile Ser Glu Met 20 25192 25 PRT Enterococcus faecalis 192 Phe Gly Lys Leu Val Trp Asp Thr ThrLeu Gln Ile Asp Leu Phe Ser 1 5 10 15 Pro Pro Glu Glu Gln Ile Ile AsnAsn 20 25 193 25 PRT Enterococcus faecium 193 Cys Ser Asp Leu Val TyrAla Thr Gly Leu Gln Leu Asn Leu Phe Glu 1 5 10 15 Asp Pro Glu Lys GlnIle Asn Glu Ala 20 25 194 25 PRT Enterococcus faecium 194 Cys Ser LysLeu Val Tyr Ser Asn Ala Leu Gln Leu Asp Leu Phe Glu 1 5 10 15 Asp ProAsn Glu Gln Val Lys Asp Leu 20 25 195 25 PRT Lactococcus lactis 195 GlyAsn Gln Leu Ser Asp Ser Ser Val Lys Gln Leu Ser Leu Phe Glu 1 5 10 15Ser Val Gln Glu Asn Gln Thr Asn Lys 20 25 196 25 PRT Lactococcus lactis196 Ala Asn Asn Leu Ile Asp Glu Pro Tyr Gln Leu Ile Ser Leu Phe Asp 1 510 15 Ser Asp Glu Glu Asn Glu Glu Thr Ile 20 25 197 25 PRT Streptococcusgordonii 197 Tyr Ser Asp Phe Val Asp Gln Glu Tyr Gly Leu Ile Ser Leu PheAsp 1 5 10 15 Asp Pro Leu Gln Val Gln Lys Glu Glu 20 25 198 25 PRTStreptococcus gordonii 198 Gly Asn Gln Leu Ser Asp Ser Ser Val Lys GlnLeu Ser Leu Phe Glu 1 5 10 15 Ser Val Gln Glu Asn Gln Thr Asn Lys 20 25199 25 PRT Streptococcus pneumoniae 199 Tyr Ser Gly Leu Val Asp Glu SerPhe Gly Leu Ile Ser Leu Phe Asp 1 5 10 15 Asp Ile Glu Lys Ile Glu LysGlu Glu 20 25 200 25 PRT Magnetospirillum magnetotacticum 200 Ala GluGlu Val Val Pro Ala Gly Ala Glu Gln Pro Arg Leu Trp Gly 1 5 10 15 AlaSer Ser Gly Glu Asp Ala Arg Ala 20 25 201 25 PRT Methylobacteriumextorquens 201 Ala Ser Arg Val Glu Pro Leu Ala Glu Arg Gln Asn Ser HisLeu Ala 1 5 10 15 Ala Gly Gln Gln Ala Pro Asp Leu Ala 20 25 202 25 PRTRhodopseudomonas palustris 202 Ala Ser Val Ser Val Ala Val Thr Glu AlaGln Arg Gly Phe Asp Thr 1 5 10 15 Thr Ala His Gln Ala Glu Asp Val Ala 2025 203 25 PRT Mesorhizobium loti 203 Val Leu Ala Ala Ala Ala Phe Asp MetAla Gln Ala Asp Leu Thr Gly 1 5 10 15 Glu Val Thr Asp Asp Gly Ala AspIle 20 25 204 25 PRT Brucella suis 204 Ala Leu Arg Ser Ser Thr Val AlaGln Arg Gln Thr Gly Leu Asp Gln 1 5 10 15 His Glu Glu Asp Glu Ala GlyPhe Ser 20 25 205 25 PRT Sinorhizobium meliloti 205 Val Leu Arg Ser GluArg Leu Asp Pro Ala Gln Gln Asp Phe Ser Gly 1 5 10 15 Ala Pro Asp GluSer Gln Leu Leu Ala 20 25 206 25 PRT Agrobacterium tumefaciens 206 AlaVal Met Thr Glu Pro Leu Glu Glu Ala Gln Lys Ala Ser Ala Leu 1 5 10 15Ile Gly Asp Asp Val Thr Asp Val Thr 20 25 207 25 PRT Agrobacteriumtumefaciens 207 Ala Thr His Ala Glu Pro Leu Val Ala Ala Gln Ala Arg SerSer Leu 1 5 10 15 Leu Asp Glu Gly Arg Ala Glu Ile Ala 20 25 208 25 PRTAgrobacterium tumefaciens 208 Ala Val Met Ala Glu Pro Leu Glu Glu ArgGln Lys Ser Ser Ser Leu 1 5 10 15 Val Glu Asp Glu Val Thr Asp Val Thr 2025 209 25 PRT Caulobacter crescentus 209 Ala Phe Ala Val Glu Pro Met AlaAla Ala Gln Ala Arg Leu Asp Ala 1 5 10 15 Asp Ala Ala Ala Ser Ala AspGlu Thr 20 25 210 25 PRT Rhodobacter capsulatus 210 Ala Thr Arg Val GluPro Leu Ala Pro Ala Gln Leu Gly Thr Thr Pro 1 5 10 15 Ala Ala Ser ProAsp Arg Leu Ala Asp 20 25 211 25 PRT Sphingomonas aromaticivorans 211Leu Pro Val Thr Glu Pro Leu Ala Ala Ser Gln Pro Thr Leu Asp Gly 1 5 1015 Ser Gly Gln Glu Thr Thr Glu Val Ala 20 25 212 25 PRT Bordetellabronchiseptica 212 Ala Pro Asp Thr Val Pro Gln Pro Ala Ala Ser Thr CysLeu Phe Pro 1 5 10 15 Glu Pro Gly Gly Thr Pro Ala Asp His 20 25 213 25PRT Bordetella parapertussis 213 Ala Pro Asp Thr Val Pro Gln Pro Ala AlaSer Thr Cys Leu Phe Pro 1 5 10 15 Glu Pro Gly Gly Thr Pro Ala Asp His 2025 214 25 PRT Burkholderia pseudomallei 214 Ala Thr Arg Val Glu Ser ValAla Pro Pro Ala Asp Asp Leu Phe Pro 1 5 10 15 Glu Pro Gly Gly Thr ArgGlu Ala Arg 20 25 215 25 PRT Burkholderia cepacia 215 Ala Asp Gln ValGly Glu Tyr Ala Gly Gln Ser Asp Thr Leu Phe Pro 1 5 10 15 Met Pro GluSer Asp Gly Asp Ser Ile 20 25 216 25 PRT Burkholderia mallei 216 Ala ThrArg Ile Glu Ser Val Ala Pro Pro Ala Asp Asp Leu Phe Pro 1 5 10 15 GluPro Gly Gly Thr Arg Glu Ala Arg 20 25 217 25 PRT Ralstonia metallidurans217 Val Glu Ala Met Glu Ile Cys Val Pro Gln Ser Asp Ser Leu Phe Pro 1 510 15 Glu Pro Gly Ala Glu Pro Ala Glu Leu 20 25 218 25 PRTAcidothiobacillus ferrooxidans 218 Ala Leu Ala Pro Gln His Trp Pro GlyArg Gln Ala Thr Trp Trp Gln 1 5 10 15 Asp Gly Val Glu Glu Ala Arg TrpGln 20 25 219 25 PRT Methylococcus capsulatus 219 Ser Ala Asp Ile GlnPro Phe Thr Leu Pro Thr Ala Asp Leu Phe Thr 1 5 10 15 Pro Gly Ala AlaGly Gly Glu Ser Trp 20 25 220 25 PRT Pseudomonas aeruginosa 220 Ala ArgGlu Leu Pro Pro Phe Thr Pro Gln His Arg Glu Leu Phe Asp 1 5 10 15 GluArg Pro Gln Gln Tyr Leu Gly Trp 20 25 221 25 PRT Pseudomonas putida 221Ala Glu Asp Leu Pro Pro Phe Val Pro Gln His Arg Glu Leu Phe Asp 1 5 1015 Glu Arg Pro Gln Gln Tyr Leu Gly Trp 20 25 222 25 PRT Pseudomonassyringae 222 Ala Arg Asp Leu Pro Asp Phe Val Pro Ala His Arg Glu Leu PheAsp 1 5 10 15 Glu Arg Val Gln Gln Thr Leu Pro Trp 20 25 223 25 PRTPseudomonas fluorescens 223 Ala Glu Asp Leu Pro Ser Phe Val Pro Gln PheGln Glu Leu Phe Asp 1 5 10 15 Asp Arg Pro Gln Gln Thr Leu Pro Trp 20 25224 19 PRT Mycobacterium avium 224 Ala Val Glu Val Val Ser Ala Glu AlaLeu Gln Leu Pro Leu Trp Gly 1 5 10 15 Gly Leu Gly 225 25 PRTMycobacterium smegmatis 225 Pro Val Glu Val Val Ser Ser Ala Ala Leu GlnLeu Pro Leu Trp Gly 1 5 10 15 Gly Ile Gly Glu Glu Asp Arg Leu Arg 20 25226 25 PRT Mycobacterium tuberculosis 226 Val Glu Thr Val Ser Ala SerGlu Gly Leu Gln Leu Pro Leu Trp Gly 1 5 10 15 Gly Leu Gly Glu Gln AspArg Leu Arg 20 25 227 25 PRT Corynebacterium diptheriae 227 Leu Arg ProTyr Glu Cys Met Arg Pro Ser Gln Pro Gln Leu Trp Gly 1 5 10 15 Thr AsnLys Ser Asp Glu Glu Ser Glu 20 25 228 25 PRT Corynebacterium glutamicum228 Pro Leu Glu Cys Val Pro Pro Asp Met Ala Ser Gly Gly Leu Trp Asp 1 510 15 Thr Gly Arg Ser Gln Gln His Val Ala 20 25 229 25 PRT Magnetococcussp. 229 Leu Leu Phe Leu Val Ser Ala Gln His Phe Gln Pro Ser Leu Phe Ala1 5 10 15 Pro Pro Pro Arg Leu Pro Asn Ser Arg 20 25 230 25 PRTPorphyromonas gingivalis 230 Ile Leu Ser Asp Leu Val Ala Glu Ala Tyr GlnLeu Asn Leu Phe Asp 1 5 10 15 Pro Ile Asp Arg Met Arg Gln Glu Arg 20 25231 25 PRT Bacteroides fragilis 231 Val Ile Ile Thr Glu Ile Thr Asp SerThr Gln Leu Gly Leu Phe Asp 1 5 10 15 Ser Val Asp Arg Glu Lys Arg LysArg 20 25 232 25 PRT Cytophaga hutchinsonii 232 Val Ser Gly Ile Val ProGlu Asp Arg Val Gln Gln Asn Leu Phe Asp 1 5 10 15 Thr Val Asp Arg SerLys His Asn Lys 20 25 233 25 PRT Cytophaga hutchinsonii 233 Val Ile AspIle Val Pro Glu Glu Lys Ile Gln Leu Asn Leu Phe Glu 1 5 10 15 Pro GlnLys Asn Ala Arg Leu His Ala 20 25 234 25 PRT Prochlorococcus marinus 234Met Gln Asp Leu Thr Asn Cys Lys Tyr Leu Gln Gln Ser Ile Ile Asn 1 5 1015 Tyr Glu Ser Gln Glu Glu Ser Lys Lys 20 25 235 25 PRT Prochlorococcusmarinus 235 Met Gln Asn Leu Gln Ser Ala Asp His Leu Gln Gln His Leu LeuVal 1 5 10 15 Ala Val His Ala Asp Glu Gln His Arg 20 25 236 25 PRTSynechococcus sp. 236 Met Gln His Leu Gln Gly Thr Glu Leu Leu Gln SerHis Leu Leu Val 1 5 10 15 Pro Leu Ser Glu Ala Gln Gln Gln Arg 20 25 23725 PRT Methylobacterium extorquens 237 Ser Thr Asp Leu Val Pro Leu GluAla Ser Gln Arg Ala Leu Ile Gly 1 5 10 15 Ala Phe Asp Arg Glu Arg GlyGly Ala 20 25 238 25 PRT Acidothiobacillus ferrooxidans 238 Leu Leu GluIle Thr Ser Ala Asp Ala Leu Gln Ala Asp Leu Phe Leu 1 5 10 15 Ser AlaGlu Glu Glu Ala Arg Ala His 20 25 239 16 PRT Legionella pneumophila 239Leu Glu Asp Leu Ile Pro Lys Lys Pro Arg Gln Leu Asp Met Phe His 1 5 1015 240 25 PRT Legionella pneumophila 240 Leu Gly Asp Leu Ile Glu Lys AsnCys Leu Gln Leu Asp Leu Phe Asn 1 5 10 15 Gln Val Ser Glu Lys Glu LeuAsn Gln 20 25 241 25 PRT Pseudomonas syringae 241 Leu Met Asp Ile CysGln Pro Gly Glu Phe Thr Asp Asp Leu Phe Thr 1 5 10 15 Ile Asp Gln ProAla Ser Ala Asp Arg 20 25 242 25 PRT Shewanella putrefaciens 242 Leu GlyAsp Phe Tyr Ala Pro Gly Val Phe Gln Leu Gly Leu Phe Asp 1 5 10 15 GluAla Lys Pro Gln Pro Lys Ser Lys 20 25 243 25 PRT Shewanella putrefaciens243 Leu Ile Glu Leu Met Pro Thr Lys His Ile Gln Tyr Asp Leu Phe His 1 510 15 Ala Pro Thr Glu Asn Pro Ala Leu Met 20 25 244 25 PRT Morganellamorganii 244 Met Leu Ser Asp Leu Gln Gly Tyr Glu Thr Gln Leu Asp Leu PheSer 1 5 10 15 Pro Ala Ala Val Arg Pro Gly Ser Glu 20 25 245 25 PRTProvidencia rettgeri 245 Leu Ser Asp Phe Tyr Asp Pro Gly Met Phe Gln ProGly Leu Phe Asp 1 5 10 15 Asp Val Ser Thr Arg Ser Asn Ser Gln 20 25 24625 PRT Escherichia coli 246 Met Leu Ala Asp Phe Ser Gly Lys Glu Ala GlnLeu Asp Leu Phe Asp 1 5 10 15 Ser Ala Thr Pro Ser Ala Gly Ser Glu 20 25247 25 PRT Escherichia coli 247 Leu Gly Asp Phe Phe Ser Gln Gly Val AlaGln Leu Asn Leu Phe Asp 1 5 10 15 Asp Asn Ala Pro Arg Pro Gly Ser Glu 2025 248 25 PRT Shigella flexneri 248 Leu Ala Asp Phe Thr Pro Ser Gly IleAla Gln Pro Gly Leu Phe Asp 1 5 10 15 Glu Ile Gln Pro Arg Lys Asn SerGlu 20 25 249 25 PRT Salmonella typhi 249 Met Leu Ser Ser Met Thr AspGly Thr Glu Gln Leu Ser Leu Phe Asp 1 5 10 15 Glu Arg Pro Ala Arg ArgGly Ser Glu 20 25 250 25 PRT Salmonella typhi 250 Leu Asn Asp Phe ThrPro Thr Gly Ile Ser Gln Leu Asn Leu Phe Asp 1 5 10 15 Glu Val Gln ProHis Glu Arg Ser Glu 20 25 251 25 PRT Salmonella typhi 251 Leu Gly GlyPhe Phe Ser Gln Gly Val Ala Gln Leu Asn Leu Phe Asp 1 5 10 15 Asp AsnAla Pro Arg Ala Gly Ser Ala 20 25 252 25 PRT Salmonella typhimurium 252Leu Ala Asp Phe Thr Pro Ser Gly Ile Ala Gln Pro Gly Leu Phe Asp 1 5 1015 Glu Ile Gln Pro Arg Lys Asn Ser Glu 20 25 253 25 PRT Salmonellatyphimurium 253 Met Leu Ala Asp Phe Ser Gly Lys Glu Ala Gln Leu Asp LeuPhe Asp 1 5 10 15 Ser Ala Thr Pro Ser Ala Gly Ser Glu 20 25 254 25 PRTSalmonella typhimurium 254 Leu Asn Asp Phe Thr Pro Thr Gly Val Ser GlnLeu Asn Leu Phe Asp 1 5 10 15 Glu Val Gln Pro Arg Glu Arg Ser Glu 20 25255 25 PRT Salmonella typhimurium 255 Leu Gly Asp Phe Phe Ser Gln GlyVal Ala Gln Leu Asn Leu Phe Asp 1 5 10 15 Asp Asn Ala Pro Arg Ala GlySer Ala 20 25 256 25 PRT Klebsiella pneumoniae 256 Leu Asn Asp Phe ThrGly Ser Gly Val Ser Gln Leu Gln Leu Phe Asp 1 5 10 15 Glu Arg Pro ProArg Pro His Ser Ala 20 25 257 25 PRT Klebsiella pneumoniae 257 Leu GlyAsp Phe Tyr Ser Gln Gly Val Ala Gln Leu Asn Leu Phe Asp 1 5 10 15 AspAsn Ala Pro Arg Lys Gly Ser Glu 20 25 258 25 PRT Klebsiella pneumoniae258 Leu Gly Asp Phe Tyr Ser Gln Gly Val Ala Gln Leu Asn Leu Phe Asp 1 510 15 Glu Leu Ala Pro Arg His Asn Ser Ala 20 25 259 25 PRT Serratiamarcescens 259 Met Leu Ser Asp Leu Gln Gly His Glu Thr Gln Leu Asp LeuPhe Ala 1 5 10 15 Pro Ala Ala Val Arg Pro Gly Ser Glu 20 25 260 25 PRTDesulfovibrio vulgaris 260 Leu Phe Gly Leu Glu Pro Ala Ala Gly Arg GlnGly Ser Leu Leu Asp 1 5 10 15 Leu Leu Asp Gly Ser His Glu His Lys 20 25261 22 PRT Magnetococcus sp. 261 Met His Thr Gly Ser Ala Gln Leu Leu IleAla Phe Pro Leu Asp Pro 1 5 10 15 Val Leu Ser Trp Glu Asn 20 262 20 PRTMagnetospirillum magnetotacticum 262 Met Ser Glu Ala Gln Leu Pro Leu AlaPhe Gly His Val Pro Ser Leu 1 5 10 15 Ala Ala Glu Asp 20 263 20 PRTRhodopseudomonas palustris 263 Val Glu Pro Arg Gln Leu Ala Leu Asp LeuPro His Ala Glu Ser Leu 1 5 10 15 Ser Arg Glu Asp 20 264 26 PRTMesorhizobium loti 264 Met Thr Ala Gln Arg Thr Asp Pro Pro Arg Gln LeuPro Leu Asp Leu 1 5 10 15 Gly His Gly Thr Gly Tyr Ser Arg Asp Glu 20 25265 23 PRT Sinorhizobium meliloti 265 Met Lys Arg His Leu Ser Glu GlnLeu Pro Leu Val Phe Gly His Ala 1 5 10 15 Pro Ala Thr Gly Arg Asp Asp 20266 26 PRT Agrobacterium tumefaciens 266 Lys Thr Asp Asn Ala Arg Ser LysAla Glu Gln Leu Pro Leu Ala Phe 1 5 10 15 Ser His Gln Ser Ala Ser GlyArg Glu Asp 20 25 267 19 PRT Caulobacter crescentus 267 Met Ser Thr GlnPhe Lys Leu Pro Leu Ala Ser Pro Leu Thr His Gly 1 5 10 15 Arg Glu Asp268 19 PRT Rhodobacter sphaeroides 268 Val Lys Gly Gln Leu Ala Phe AspLeu Pro Ile Arg Pro Ala Leu Ser 1 5 10 15 Arg Glu Asp 269 19 PRTRhodobacter capsulatus 269 Met Thr Arg Gln Leu Pro Leu Pro Leu Pro ValArg Val Ala Glu Gly 1 5 10 15 Arg Glu Asp 270 18 PRT Rickettsia conorii270 Val Gln Gln Tyr Ile Phe Arg Phe Thr Thr Ser Ser Lys Tyr His Pro 1 510 15 Asp Glu 271 18 PRT Rickettsia prowazekii 271 Met Gln Gln Tyr IlePhe His Phe Thr Pro Ser Asn Lys Tyr His Pro 1 5 10 15 Asp Glu 272 25 PRTWolbachia sp. 272 Arg Lys Arg Leu Arg Lys Arg Phe Asn Val Gln Leu AsnLeu Phe Asn 1 5 10 15 Asn Asn Gln Ala Asp Tyr Ser Arg Gln 20 25 273 18PRT Neisseria gonorrhoeae 273 Met Asn Gln Leu Ile Phe Asp Phe Ala AlaHis Asp Tyr Pro Ser Phe 1 5 10 15 Asp Lys 274 18 PRT Neisseriameningitidis 274 Met Asn Gln Leu Ile Phe Asp Phe Ala Ala His Asp Tyr ProSer Phe 1 5 10 15 Asp Lys 275 18 PRT Nitrosomonas europaea 275 Met ArgGln Gln Leu Leu Asp Ile Thr Glu Ile Gly Pro Pro Ser Leu 1 5 10 15 AspAsn 276 19 PRT Bordetella parapertussis 276 Met Asn Arg Gln Leu Leu LeuAsp Val Leu Pro Ala Pro Ala Pro Thr 1 5 10 15 Leu Asn Asn 277 19 PRTBurkholderia fungorum 277 Val Leu Arg Gln Leu Thr Leu Asp Leu Gly ThrPro Pro Pro Ser Thr 1 5 10 15 Phe Asp Asn 278 19 PRT Burkholderiapseudomallei 278 Val Thr Arg Gln Leu Thr Leu Asp Leu Gly Thr Pro Pro ProSer Thr 1 5 10 15 Phe Asp Asn 279 19 PRT Burkholderia mallei 279 Val ThrArg Gln Leu Thr Leu Asp Leu Gly Thr Pro Pro Pro Ser Thr 1 5 10 15 PheAsp Asn 280 22 PRT Ralstonia metallidurans 280 Met Ser Pro Arg Gln LysGln Leu Ser Leu Glu Leu Gly Ser Pro Pro 1 5 10 15 Pro Ser Thr Phe GluAsn 20 281 20 PRT Acidothiobacillus ferrooxidans 281 Met Gly Asn Arg GlnArg Ile Leu Pro Leu Gly Val Gln Ala Pro Ala 1 5 10 15 Thr Leu Glu Gly 20282 20 PRT Xylella fastidiosa 282 Met Ser Val Ser Gln Leu Pro Leu AlaLeu Arg Tyr Ser Ser Asp Gln 1 5 10 15 Arg Phe Glu Thr 20 283 19 PRTLegionella pneumophila 283 Met Asn Lys Gln Leu Ala Leu Ala Ile Lys LeuAsn Asp Glu Ala Thr 1 5 10 15 Leu Asp Asp 284 19 PRT Coxiella burnetii284 Met Ile Asp Gln Leu Pro Leu Arg Val Gln Leu Arg Glu Glu Thr Thr 1 510 15 Phe Ala Asn 285 19 PRT Methylococcus capsulatus 285 Met Ala GlnGln Ile Pro Leu His Phe Ala Val Asp Pro Leu Gln Thr 1 5 10 15 Phe GluAla 286 20 PRT Pseudomonas aeruginosa 286 Met Lys Pro Ile Gln Leu ProLeu Ser Val Arg Leu Arg Asp Asp Ala 1 5 10 15 Thr Phe Ala Asn 20 287 21PRT Pseudomonas putida 287 Met Lys Pro Pro Ile Gln Leu Pro Leu Gly ValArg Leu Arg Asp Asp 1 5 10 15 Ala Thr Phe Ile Asn 20 288 20 PRTPseudomonas syringae 288 Met Lys Pro Ile Gln Leu Pro Leu Ser Val Arg LeuArg Asp Asp Ala 1 5 10 15 Thr Phe Val Asn 20 289 20 PRT Pseudomonasfluorescens 289 Met Lys Pro Ile Gln Leu Pro Leu Gly Val Arg Leu Arg AspAsp Ala 1 5 10 15 Thr Phe Ile Asn 20 290 26 PRT Shewanella putrefaciens290 Asp Val Arg Val Pro Leu Asn Ser Pro Leu Gln Leu Ser Leu Pro Val 1 510 15 Tyr Leu Pro Asp Asp Glu Thr Phe Asn Ser 20 25 291 26 PRTPasteurella multocida 291 Phe Val Gly Cys Phe Leu Leu Glu Asn Phe GlnLeu Pro Leu Pro Ile 1 5 10 15 His Gln Leu Asp Asp Glu Thr Leu Asp Asn 2025 292 19 PRT Haemophilus influenzae 292 Met Asn Lys Gln Leu Pro Leu ProIle His Gln Ile Asp Asp Ala Thr 1 5 10 15 Leu Glu Asn 293 26 PRTHaemophilus ducreyi 293 Asn Trp Ser Ile Arg Phe Lys Asn Ser Leu Gln LeuLeu Leu Pro Ile 1 5 10 15 His Gln Ile Asp Asp Glu Thr Leu Asp Ser 20 25294 22 PRT Actinobacillus actinomycetemcomitans 294 Met Ser Glu Pro HisPhe Gln Leu Pro Leu Pro Ile His Gln Leu Asp 1 5 10 15 Asp Asp Thr LeuGlu Asn 20 295 25 PRT Escherichia coli 295 Val Glu Val Ser Leu Asn ThrPro Ala Gln Leu Ser Leu Pro Leu Tyr 1 5 10 15 Leu Pro Asp Asp Glu ThrPhe Ala Ser 20 25 296 25 PRT Salmonella typhi 296 Val Glu Val Ser LeuAsn Thr Pro Ala Gln Leu Ser Leu Pro Leu Tyr 1 5 10 15 Leu Pro Asp AspGlu Thr Phe Ala Ser 20 25 297 25 PRT Salmonella typhimurium 297 Val GluVal Ser Leu Asn Thr Pro Ala Gln Leu Ser Leu Pro Leu Tyr 1 5 10 15 LeuPro Asp Asp Glu Thr Phe Ala Ser 20 25 298 26 PRT Yersinia pestis 298 MetVal Glu Val Leu Leu Asn Thr Pro Ala Gln Leu Ser Leu Pro Leu 1 5 10 15Tyr Leu Pro Asp Asp Glu Thr Phe Ala Ser 20 25 299 26 PRT Geobactersulfurreducens 299 Ala Arg Ser Ser Arg Pro Phe Pro Ala Met Gln Leu ValPhe Asp Phe 1 5 10 15 Pro Val Thr Pro Lys Tyr Ser Phe Asp Asn 20 25 30016 PRT Nostoc punctiforme 300 Pro Trp Asn Asn Leu Glu His Pro Pro AsnGln Leu Ser Leu Trp Ser 1 5 10 15 301 15 PRT Anabaena sp. 301 Pro TrpAsn His Leu Asp Tyr Pro Pro His Gln Leu Asn Leu Trp 1 5 10 15 302 15 PRTPseudomonas aeruginosa 302 Pro Glu Pro Ile Pro Ala Pro Glu Val Glu GlnLeu Gly Leu Leu 1 5 10 15 303 15 PRT Pseudomonas putida 303 Pro Glu LeuPro Arg Ala Pro Glu Val Glu Gln Leu Gly Leu Leu 1 5 10 15 304 15 PRTPseudomonas syringae 304 Pro Glu Leu Asp Arg Gly Pro Gln Val Glu Gln LeuGly Leu Leu 1 5 10 15 305 15 PRT Pseudomonas fluorescens 305 Pro Glu LeuTyr Arg Glu Pro Ala Ala Glu Gln Leu Gly Leu Leu 1 5 10 15 306 16 PRTShewanella putrefaciens 306 Leu Asp Lys Lys Pro Glu Glu Thr Ser Thr GlnMet Gly Leu Ser Trp 1 5 10 15 307 15 PRT Vibrio cholerae 307 Ala Pro PhePro Val Thr Pro Glu Gln Pro Gln Leu Ser Met Phe 1 5 10 15 308 15 PRTPasteurella multocida 308 Val Lys Pro Lys Pro Glu Phe Leu Thr Gly GlnGln Ser Leu Phe 1 5 10 15 309 15 PRT Escherichia coli 309 Glu Ile GlyAla Val Pro Ala Ile Pro Gln Gln Ser Ser Leu Phe 1 5 10 15 310 15 PRTSalmonella typhi 310 Glu Ile Gly Thr Ala Pro Ser Ile Pro Gln Gln Ser SerLeu Phe 1 5 10 15 311 15 PRT Salmonella typhimurium 311 Glu Ile Gly ThrAla Pro Ser Ile Pro Gln Gln Ser Ser Leu Phe 1 5 10 15 312 15 PRTYersinia pestis 312 Thr Leu Pro Thr Ala Pro Asp Trp Pro Glu Gln Glu ThrLeu Phe 1 5 10 15 313 16 PRT Bacillus halodurans 313 Glu Ile Glu Tyr ArgGly Leu Thr Pro Lys Gln Leu Asn Leu Phe Glu 1 5 10 15 314 15 PRTBacillus stearothermophilus 314 Gly Ile Glu Tyr Thr Gly Leu Ala Pro ArgGln Leu Gly Leu Phe 1 5 10 15 315 15 PRT Bacillus subtilis 315 Asp IleGlu Tyr Ser Gly Leu Ala Pro Arg Gln Leu Asp Leu Phe 1 5 10 15 316 15 PRTStaphylococcus aureus 316 Asn Ile Glu Tyr Glu Gly Leu Ala Pro Gln GlnLeu Lys Leu Phe 1 5 10 15 317 15 PRT Staphylococcus epidermidis 317 AspIle Asp Tyr Glu Gly Leu Ala Pro Gln Gln Leu Lys Leu Phe 1 5 10 15 318 16PRT Bacillus anthracis 318 Asn Ile Thr Tyr Gly Glu Pro Lys Pro Glu GlnLeu Asn Leu Phe Glu 1 5 10 15 319 17 PRT Listeria innocua 319 Gln ValGlu Phe Gln Gly Leu Ala Pro Met Gln Met Asp Leu Phe Ser 1 5 10 15 Glu320 17 PRT Listeria monocytogenes 320 Gln Val Glu Phe Gln Gly Leu AlaPro Met Gln Met Asp Leu Phe Ser 1 5 10 15 Glu 321 15 PRT Pediococcusacidilactici 321 Gly Ile His Phe Thr Gly Leu Gly Pro Met Gln Leu Asp LeuPhe 1 5 10 15 322 15 PRT Enterococcus faecalis 322 Asn Leu Ser Tyr AspAsp Leu Asn Pro Lys Gln Leu Asp Leu Phe 1 5 10 15 323 15 PRTEnterococcus faecium 323 Asn Ile Lys Pro Asp Gly Leu Asn Pro Thr Gln MetAsp Leu Phe 1 5 10 15 324 25 PRT Magnetococcus sp. 324 Gln Gly His AlaPro Ala Ser Gln Pro Tyr Gln Leu Thr Leu Phe Glu 1 5 10 15 Asp Ala ProPro Ser Pro Ala Leu Leu 20 25 325 25 PRT Aquifex aeolicus 325 Arg GluLeu Glu Glu Lys Glu Asn Lys Lys Glu Asp Ile Val Pro Leu 1 5 10 15 LeuGlu Glu Thr Phe Lys Lys Ser Glu 20 25 326 25 PRT Aquifex pyrophilus 326Leu Lys Glu Leu Glu Gly Glu Lys Gly Lys Gln Glu Val Leu Pro Phe 1 5 1015 Leu Glu Glu Thr Tyr Lys Lys Ser Val 20 25 327 17 PRT Thermotogamaritima 327 Lys Asn Gly Lys Ser Asn Arg Phe Ser Gln Gln Ile Pro Leu PhePro 1 5 10 15 Val 328 25 PRT Chloroflexus aurantiacus 328 Val Pro AlaGln Glu Thr Gly Gln Gly Met Gln Leu Ser Phe Phe Asp 1 5 10 15 Leu AlaPro His Pro Val Val Glu Tyr 20 25 329 25 PRT Porphyromonas gingivalis329 Asp Glu Lys Gly Arg Ser Ile Asp Gly Tyr Gln Leu Ser Phe Phe Gln 1 510 15 Leu Asp Asp Pro Val Leu Ser Gln Ile 20 25 330 25 PRT Bacteroidesfragilis 330 Ala Glu Val Ser Glu Asn Arg Gly Gly Met Gln Leu Ser Phe PheGln 1 5 10 15 Leu Asp Asp Pro Ile Leu Cys Gln Ile 20 25 331 25 PRTCytophaga hutchinsonii 331 Lys Leu Lys Glu Val Pro Lys Ser Thr Leu GlnMet Ser Leu Phe Glu 1 5 10 15 Ala Ala Asp Pro Ala Trp Asp Ser Ile 20 25332 25 PRT Chlorobium tepidum 332 Gln Ala Leu Pro Leu Arg Val Glu SerArg Gln Ile Ser Leu Phe Glu 1 5 10 15 Glu Glu Glu Ser Arg Leu Arg LysAla 20 25 333 15 PRT Chlamydia trachomatis 333 Asp Leu Arg Pro Glu ProGlu Lys Ala Gln Gln Leu Val Met Phe 1 5 10 15 334 15 PRT Chlamydophilapneumoniae 334 Ile Thr Arg Pro Ala Gln Asp Lys Met Gln Gln Leu Thr LeuPhe 1 5 10 15 335 17 PRT Synechocystis sp. 335 Ala Ala Glu Ala Ala GluAsp Gln Ala Lys Gln Leu Asp Ile Phe Gly 1 5 10 15 Phe 336 25 PRTFibrobacter succinogenes 336 Ala Gln Asn Lys Lys Ile Lys Ala Gln Pro GlnMet Asp Leu Phe Ala 1 5 10 15 Pro Pro Asp Glu Asn Thr Leu Leu Leu 20 25337 25 PRT Treponema denticola 337 Glu Lys Thr Pro Ser Ser Pro Ala GluLys Gly Leu Ser Leu Phe Pro 1 5 10 15 Glu Glu Glu Leu Ile Leu Asn GluIle 20 25 338 25 PRT Treponema pallidum 338 Ala Ala Ser Lys Pro Cys AlaGln Arg Val Ser Ala Asp Leu Phe Thr 1 5 10 15 Gln Glu Glu Leu Ile GlyAla Glu Ile 20 25 339 25 PRT Borrelia burgdorferi 339 Val Gly Arg GluGly Asn Ser Cys Leu Glu Phe Leu Pro His Val Ser 1 5 10 15 Ser Asp GlyAsn Asp Lys Glu Ile Leu 20 25 340 25 PRT Magnetospirillummagnetotacticum 340 Gln Ala Ser Gly Met Ala Arg Leu Ala Asp Asp Leu ProLeu Phe Ala 1 5 10 15 Ala Leu Ala Lys Pro Val Ala Ala Ser 20 25 341 25PRT Magnetospirillum magnetotacticum 341 Arg Glu Arg Pro Thr Arg Arg ArgIle Glu Asp Leu Pro Leu Phe Ala 1 5 10 15 Ser Leu Ala Ala Ala Pro ProPro Pro 20 25 342 25 PRT Rhodopseudomonas palustris 342 Asp Arg Gly GlnPro Lys Thr Leu Ile Asp Asp Leu Pro Leu Phe Ala 1 5 10 15 Ile Thr AlaArg Ala Pro Ala Glu Ala 20 25 343 25 PRT Mesorhizobium loti 343 Val SerGly Lys Thr Asn Arg Leu Val Asp Asp Leu Pro Leu Phe Ser 1 5 10 15 ValAla Met Lys Arg Glu Ala Pro Lys 20 25 344 25 PRT Brucella suis 344 ThrSer Gly Lys Ala Asp Arg Leu Ile Asp Asp Leu Pro Leu Phe Ser 1 5 10 15Val Met Leu Gln Gln Glu Lys Pro Lys 20 25 345 25 PRT Sinorhizobiummeliloti 345 Arg Lys Asn Pro Ala Ser Gln Leu Ile Asp Asp Leu Pro Leu PheGln 1 5 10 15 Val Ala Val Arg Arg Glu Glu Ala Ala 20 25 346 25 PRTAgrobacterium tumefaciens 346 Arg Lys Asn Pro Ala Ser Gln Leu Ile AspAsp Leu Pro Leu Phe Gln 1 5 10 15 Ile Ala Val Arg Arg Glu Glu Thr Arg 2025 347 25 PRT Caulobacter crescentus 347 Ser Lys Asp Gln Ser Pro Ala LysLeu Asp Asp Leu Pro Leu Phe Ala 1 5 10 15 Val Ser Gln Ala Val Ala ValThr Ser 20 25 348 25 PRT Rhodobacter sphaeroides 348 Ser Gly Gly Arg ArgGln Thr Leu Ile Asp Asp Leu Pro Leu Phe Arg 1 5 10 15 Ala Ala Pro ProPro Pro Ala Pro Ala 20 25 349 25 PRT Rickettsia conorii 349 Gly Lys AsnIle Leu Ser Thr Glu Ser Asn Asn Leu Ser Leu Phe Tyr 1 5 10 15 Leu GluPro Asn Lys Thr Thr Ile Ser 20 25 350 25 PRT Rickettsia prowazekii 350Glu Lys Asn Ile Leu Ser Asn Ala Ser Asn Asn Leu Ser Leu Phe Asn 1 5 1015 Phe Glu His Glu Lys Pro Ile Ser Asn 20 25 351 25 PRT Sphingomonasaromaticivorans 351 Ala Thr Gly Gly Leu Ala Ala Gly Leu Asp Asp Leu ProLeu Phe Ala 1 5 10 15 Ala Ala Ile Glu Ala Ala Glu Glu Lys 20 25 352 25PRT Neisseria gonorrhoeae 352 Leu Glu Asn Gln Ala Ala Ala Asn Arg ProGln Leu Asp Ile Phe Ser 1 5 10 15 Thr Met Pro Ser Glu Lys Gly Asp Glu 2025 353 25 PRT Neisseria meningitidis 353 Leu Glu Asn Gln Ala Ala Ala AsnArg Pro Gln Leu Asp Ile Phe Ser 1 5 10 15 Thr Met Pro Ser Glu Lys GlyAsp Glu 20 25 354 25 PRT Nitrosomonas europaea 354 Leu Glu Gln Glu ThrLeu Ser Arg Ser Pro Gln Gln Thr Leu Phe Glu 1 5 10 15 Thr Val Glu GluAsn Ala Lys Ala Val 20 25 355 25 PRT Bordetella bronchiseptica 355 ArgLeu Glu Ala Gln Gly Ala Pro Thr Pro Gln Leu Gly Leu Phe Ala 1 5 10 15Ala Ala Leu Asp Ala Asp Val Gln Ser 20 25 356 25 PRT Bordetellapertussis 356 Arg Leu Glu Ala Gln Gly Ala Pro Thr Pro Gln Leu Gly LeuPhe Ala 1 5 10 15 Ala Ala Leu Asp Ala Asp Val Gln Ser 20 25 357 25 PRTBurkholderia pseudomallei 357 Glu Gln Gln Ser Ala Ala Gln Ala Thr ProGln Leu Asp Leu Phe Ala 1 5 10 15 Ala Pro Pro Val Val Asp Glu Pro Glu 2025 358 25 PRT Burkholderia cepacia 358 Glu Gln Gln Ser Ala Ala Gln ProAla Pro Gln Leu Asp Leu Phe Ala 1 5 10 15 Ala Pro Met Pro Met Leu LeuGlu Asp 20 25 359 25 PRT Burkholderia mallei 359 Glu Gln Gln Ser Ala AlaGln Ala Thr Pro Gln Leu Asp Leu Phe Ala 1 5 10 15 Ala Pro Pro Val ValAsp Glu Pro Glu 20 25 360 25 PRT Ralstonia metallidurans 360 Glu Gln SerAla Asp Ala Thr Pro Thr Pro Gln Met Asp Leu Phe Ser 1 5 10 15 Ala GlnSer Ser Pro Ser Ala Asp Asp 20 25 361 25 PRT Acidothiobacillusferrooxidans 361 Arg Ser Ser Leu Ser His Thr Ala Pro Ala Gln Leu Ser LeuPhe Gln 1 5 10 15 Ala Ala Pro His Pro Ala Val Tyr Arg 20 25 362 25 PRTXylella fastidiosa 362 Ile Thr Pro Leu Ala Leu Asp Ala Pro Gln Gln CysSer Leu Phe Ala 1 5 10 15 Ser Ala Pro Ser Ala Ala Gln Glu Ala 20 25 36325 PRT Xylella fastidiosa 363 Ile Thr Pro Leu Ala Leu Asp Ala Pro GlnGln Cys Ser Leu Phe Ala 1 5 10 15 Ser Ala Pro Ser Ala Ala Gln Glu Ala 2025 364 25 PRT Xylella fastidiosa 364 Ile Thr Pro Leu Ala Leu Asp Ala ProGln Gln Cys Ser Leu Phe Ala 1 5 10 15 Ser Ala Pro Ser Ala Ala Gln GluAla 20 25 365 25 PRT Legionella pneumophila 365 Gln Ile Gln Asp Thr GlnSer Ile Leu Val Gln Thr Gln Ile Ile Lys 1 5 10 15 Pro Pro Thr Ser ProVal Leu Thr Glu 20 25 366 25 PRT Coxiella burnetii 366 Pro Val Ile SerGlu Thr Gln Gln Pro Gln Gln Asn Glu Leu Phe Leu 1 5 10 15 Pro Ile GluAsn Pro Val Leu Thr Gln 20 25 367 25 PRT Methylococcus capsulatus 367Ser Ala His Gln Gln Ala Ala Pro Val Ala Gln Leu Asp Leu Phe Leu 1 5 1015 Pro Pro Val Val Asp Glu Pro Glu Cys 20 25 368 25 PRT Pseudomonasaeruginosa 368 Gln Gln Ser Gly Lys Pro Ala Ser Pro Met Gln Ser Asp LeuPhe Ala 1 5 10 15 Ser Leu Pro His Pro Val Ile Asp Glu 20 25 369 25 PRTAzotobacter vinelandii 369 Arg Glu Ala Gly Lys Pro Gln Pro Pro Ile GlnSer Asp Leu Phe Ala 1 5 10 15 Ser Leu Pro His Pro Leu Met Glu Glu 20 25370 25 PRT Pseudomonas putida 370 Lys Ala Lys Asp Ala Pro Gln Val ProHis Gln Ser Asp Leu Phe Ala 1 5 10 15 Ser Leu Pro His Pro Ala Ile GluLys 20 25 371 25 PRT Pseudomonas syringae 371 Ala Lys Pro Gly Lys ProAla Ile Pro Gln Gln Ser Asp Met Phe Ala 1 5 10 15 Ser Leu Pro His ProVal Leu Asp Glu 20 25 372 25 PRT Pseudomonas fluorescens 372 Ala Ala LysGly Lys Pro Ala Ala Pro Gln Gln Ser Asp Met Phe Ala 1 5 10 15 Ser LeuPro His Pro Val Leu Asp Glu 20 25 373 25 PRT Shewanella putrefaciens 373His Gln Val Glu Gly Thr Lys Thr Pro Ile Gln Thr Leu Leu Ala Leu 1 5 1015 Pro Glu Pro Val Glu Asn Pro Ala Val 20 25 374 25 PRT Vibrioparahaemolyticus 374 Pro Arg Pro Ser Thr Val Asp Val Ala Asn Gln Leu SerLeu Ile Pro 1 5 10 15 Glu Pro Ser Glu Ile Glu Gln Ala Leu 20 25 375 25PRT Vibrio cholerae 375 Arg Lys Pro Ser Arg Val Asp Ile Ala Asn Gln LeuSer Leu Ile Pro 1 5 10 15 Glu Pro Ser Ala Val Glu Gln Ala Leu 20 25 37625 PRT Pasteurella multocida 376 Asp Leu Arg Gln Leu Asn Gln Thr Gln GlyGlu Leu Ala Leu Met Glu 1 5 10 15 Glu Asp Asp Ser Lys Thr Ala Val Trp 2025 377 25 PRT Haemophilus influenzae 377 Ile Gln Asp Leu Arg Leu Leu AsnGln Arg Gln Gly Glu Leu Phe Phe 1 5 10 15 Glu Gln Glu Thr Asp Ala LeuArg Glu 20 25 378 25 PRT Haemophilus ducreyi 378 Gln Gln Thr Lys Met AlaGln Gln His Pro Gln Ala Asp Leu Leu Phe 1 5 10 15 Thr Val Glu Met ProGlu Glu Glu Lys 20 25 379 25 PRT Actinobacillus actinomycetemcomitans379 Ile Gln Asp Leu Arg Leu Leu Asn Gln Arg Gln Gly Glu Leu Ala Phe 1 510 15 Glu Ser Ala Glu Asp Glu Asn Lys Asp 20 25 380 25 PRT Escherichiacoli 380 Asn Ala Ala Ala Thr Gln Val Asp Gly Thr Gln Met Ser Leu Leu Ser1 5 10 15 Val Pro Glu Glu Thr Ser Pro Ala Val 20 25 381 25 PRTSalmonella enteritidis 381 Asn Ala Ala Ala Thr Gln Val Asp Gly Thr GlnMet Ser Leu Leu Ala 1 5 10 15 Ala Pro Glu Glu Thr Ser Pro Ala Val 20 25382 25 PRT Salmonella typhi 382 Asn Ala Ala Ala Thr Gln Val Asp Gly ThrAla Met Ser Leu Leu Ala 1 5 10 15 Ala Pro Glu Glu Thr Ser Pro Ala Val 2025 383 25 PRT Salmonella typhimurium 383 Asn Ala Ala Ala Thr Gln Val AspGly Thr Gln Met Ser Leu Leu Ala 1 5 10 15 Ala Pro Glu Glu Thr Ser ProAla Val 20 25 384 25 PRT Yersinia pestis 384 Asn Ala Ala Ala Ser Thr IleAsp Gly Ser Gln Met Thr Leu Leu Asn 1 5 10 15 Glu Glu Ile Pro Pro AlaVal Glu Ala 20 25 385 25 PRT Yersinia pseudotuberculosis 385 Asn Ala AlaAla Ser Thr Ile Asp Gly Ser Gln Met Thr Leu Leu Asn 1 5 10 15 Glu GluIle Pro Pro Ala Val Glu Ala 20 25 386 25 PRT Geobacter sulfurreducens386 Lys Arg Ala Gly Ala Pro Lys Pro Ser Pro Gln Leu Ser Leu Phe Asp 1 510 15 Gln Gly Asp Asp Leu Leu Arg Arg Arg 20 25 387 25 PRTDesulfitobacterium hafniense 387 Glu His Leu Leu Asn Lys Glu Lys Ala ThrGln Leu Ser Leu Phe Glu 1 5 10 15 Val Gln Pro Leu Asp Pro Leu Leu Gln 2025 388 25 PRT Clostridium difficile 388 Glu Asp Ser Val Lys Glu Val AlaLeu Thr Gln Ile Ser Phe Asp Ser 1 5 10 15 Val Asn Arg Asp Ile Leu SerGlu Glu 20 25 389 25 PRT Carboxydothermus hydrogenoformans 389 Gly LeuLys Val Lys Asp Thr Val Pro Val Gln Leu Ser Leu Phe Glu 1 5 10 15 GluLys Pro Glu Pro Ser Gly Val Ile 20 25 390 25 PRT Bacillus halodurans 390Lys Glu Val Ala Ser Thr Asn Glu Pro Thr Gln Leu Ser Leu Phe Glu 1 5 1015 Pro Glu Pro Leu Glu Ala Tyr Lys Pro 20 25 391 25 PRT Bacillusstearothermophilus 391 Glu Gly Val Leu Ala Glu Ala Ala Phe Glu Gln LeuSer Met Phe Pro 1 5 10 15 Asp Leu Ala Pro Ala Pro Val Glu Pro 20 25 39225 PRT Bacillus subtilis 392 Gln Lys Pro Gln Val Lys Glu Glu Pro Ala GlnLeu Ser Phe Phe Asp 1 5 10 15 Glu Ala Glu Lys Pro Ala Glu Thr Pro 20 25393 25 PRT Staphylococcus aureus 393 Thr Leu Ser Gln Lys Asp Phe Glu GlnAla Ser Phe Asp Leu Phe Glu 1 5 10 15 Asn Asp Gln Lys Ser Glu Ile GluLeu 20 25 394 25 PRT Staphylococcus epidermidis 394 His Thr Ser Asn HisAsn Tyr Glu Gln Ala Thr Phe Asp Leu Phe Asp 1 5 10 15 Gly Tyr Asn GlnGln Ser Glu Val Glu 20 25 395 25 PRT Bacillus anthracis 395 Glu Thr LysVal Asp Asn Glu Glu Glu Ser Gln Leu Ser Phe Phe Gly 1 5 10 15 Ala GluGln Ser Ser Lys Lys Gln Asp 20 25 396 25 PRT Listeria innocua 396 LysGln Pro Glu Glu Ile His Glu Glu Val Gln Leu Ser Met Phe Pro 1 5 10 15Val Glu Pro Glu Glu Lys Ala Ser Ser 20 25 397 25 PRT Listeriamonocytogenes 397 Lys Gln Pro Glu Glu Val His Glu Glu Val Gln Leu SerMet Phe Pro 1 5 10 15 Leu Glu Pro Glu Lys Lys Ala Ser Ser 20 25 398 25PRT Enterococcus faecalis 398 Glu Val Ser Glu Val His Glu Glu Thr GluGln Leu Ser Leu Phe Lys 1 5 10 15 Glu Val Ser Thr Glu Glu Leu Ser Val 2025 399 25 PRT Enterococcus faecium 399 Ile Gln Asp Arg Val Lys Glu GluAsn Gln Gln Leu Ser Leu Phe Ser 1 5 10 15 Glu Leu Ser Glu Asn Glu ThrGlu Val 20 25 400 25 PRT Streptococcus equi 400 Val Arg Glu Thr Gln GlnLeu Ala Asn Gln Gln Leu Ser Leu Phe Thr 1 5 10 15 Asp Asp Gly Ser SerSer Glu Ile Ile 20 25 401 25 PRT Streptococcus pyogenes 401 Val Glu SerSer Ser Ala Val Arg Gln Gly Gln Leu Ser Leu Phe Gly 1 5 10 15 Asp GluGlu Lys Ala His Glu Ile Arg 20 25 402 25 PRT Streptococcus mutans 402Glu Thr Lys Glu Ser Gln Pro Val Glu Glu Gln Leu Ser Leu Phe Ala 1 5 1015 Ile Asp Asn Asn Tyr Glu Glu Leu Ile 20 25 403 25 PRT Streptococcuspneumoniae 403 Pro Met Arg Gln Thr Ser Ala Val Thr Glu Gln Ile Ser LeuPhe Asp 1 5 10 15 Arg Ala Glu Glu His Pro Ile Leu Ala 20 25 404 25 PRTClostridium acetobutylicum 404 Val Lys Glu Glu Pro Lys Lys Asp Ser TyrGln Ile Asp Phe Asn Tyr 1 5 10 15 Leu Glu Arg Glu Ser Ile Leu Lys Glu 2025 405 25 PRT Chlorobium tepidum 405 Lys Pro Gln Asp Phe Ser Ser Ile PheSer Ala Asp Thr Leu Phe Ala 1 5 10 15 Phe Ser Pro Glu Gly Ile Lys ValIle 20 25 406 15 PRT Anabaena sp. 406 Ala Pro Thr Thr Leu Glu Ser AsnLys Arg Gln Leu Ser Leu Phe 1 5 10 15 407 15 PRT Burkholderia cepacia407 Arg Asp Asp Phe Thr Ala Leu Met Ser Gly Gln Lys Pro Leu Phe 1 5 1015 408 17 PRT Ralstonia metallidurans 408 Asp Asp Asp Phe Glu Thr LeuLeu Thr Gly Gln Met Thr Leu Phe Pro 1 5 10 15 Gln 409 15 PRT Pseudomonasaeruginosa 409 Gly Asp Asp Phe Ala Thr Leu Val Asp Arg Gln Met Ala LeuPhe 1 5 10 15 410 15 PRT Pseudomonas putida 410 Gly Asp Asp Phe Ala ArgLeu Thr Asp His Gln Leu Leu Leu Phe 1 5 10 15 411 15 PRT Pseudomonassyringae 411 Asp Asp Asp Phe Ser Thr Leu Ile Gly Gly Gln Leu Gly Leu Phe1 5 10 15 412 15 PRT Pseudomonas fluorescens 412 Asp Asp Asp Phe Ser ThrLeu Ile Gly Gly Gln Leu Gly Leu Phe 1 5 10 15 413 15 PRT Shewanellaputrefaciens 413 Lys Leu Asn Tyr Thr Asn Ile Ala Ser Lys Gln Leu Ser LeuIle 1 5 10 15 414 15 PRT Vibrio cholerae 414 Gly Lys Gln Phe Asp Glu LeuIle Ala Pro Gln Leu Gly Leu Phe 1 5 10 15 415 15 PRT Escherichia coli415 Glu Asp Asn Phe Ala Thr Leu Met Thr Gly Gln Leu Gly Leu Phe 1 5 1015 416 15 PRT Salmonella typhi 416 Glu Asp Asn Phe Ala Thr Leu Leu ThrGly Gln Leu Gly Leu Phe 1 5 10 15 417 15 PRT Salmonella typhimurium 417Glu Asp Asn Phe Ala Thr Val Leu Thr Gly Gln Leu Gly Leu Phe 1 5 10 15418 15 PRT Klebsiella pneumoniae 418 Asn Asp Asn Phe Ala Thr Ile Val ThrGly Gln Leu Gly Leu Phe 1 5 10 15 419 15 PRT Yersinia pestis 419 Gln AspAsp Phe Thr Thr Leu Ile Thr Gly Gln Met Gly Leu Phe 1 5 10 15 420 16 PRTGeobacter sulfurreducens 420 Met Lys Lys Phe Ala Pro Phe Leu Pro Arg GluArg Thr Leu Phe Asp 1 5 10 15 421 25 PRT Magnetococcus sp. 421 Thr GlnHis Gln Lys Asp Gln Lys Leu Gly Phe Met Asn Leu Phe Gly 1 5 10 15 AspGlu Glu Ala Glu Asn Ser Glu Ser 20 25 422 25 PRT Aquifex aeolicus 422Ala Asn Ser Glu Lys Ala Leu Met Ala Thr Gln Asn Ser Leu Phe Gly 1 5 1015 Ala Pro Lys Glu Glu Val Glu Glu Leu 20 25 423 25 PRT Thermotogamaritima 423 Asn Lys Arg Val Glu Lys Asp Ile Leu Glu Ile Arg Ser Leu PheGly 1 5 10 15 Glu Lys Val Glu Gln Glu Ser Ser Asn 20 25 424 25 PRTChloroflexus aurantiacus 424 Ile Glu Ala Gln Lys Ala Arg Glu Ile Gly GlnSer Ser Leu Phe Asp 1 5 10 15 Ile Phe Gly Glu Ala Thr Thr Ala Asn 20 25425 25 PRT Thermus aquaticus 425 Ala Glu Thr Arg Glu Arg Gly Arg Ser GlyLeu Val Gly Leu Phe Ala 1 5 10 15 Glu Val Glu Glu Pro Pro Leu Val Glu 2025 426 25 PRT Deinococcus radiodurans 426 Ala Glu Ile Asn Ala Arg AlaGln Ser Gly Met Ser Met Met Phe Gly 1 5 10 15 Met Glu Glu Val Lys LysGlu Arg Pro 20 25 427 25 PRT Porphyromonas gingivalis 427 Ser Val ValGln Glu Glu Lys His Ser Gln Ser Asn Ser Leu Phe Gly 1 5 10 15 Glu GluGlu Asp Leu Met Ile Pro Arg 20 25 428 25 PRT Bacteroides fragilis 428Asn Arg Tyr Gln Ala Asp Lys Ala Ala Ala Val Asn Ser Leu Phe Gly 1 5 1015 Gly Asp Asn Val Ile Asp Ile Ala Thr 20 25 429 25 PRT Cytophagahutchinsonii 429 Asn Ala Phe Gln Thr Glu Asp Asp Ser Asn Gln Ser Ser LeuPhe Gly 1 5 10 15 Asp Ser Ser Ser Ala Lys Pro Ala Pro 20 25 430 25 PRTChlorobium tepidum 430 Gln Ile Gln Asn Lys Ala Val Thr Leu Gly Gln GlyGly Phe Phe Asn 1 5 10 15 Asp Asp Phe Ser Asp Gly Gln Ala Gly 20 25 43125 PRT Chlamydia trachomatis 431 Ser Arg Glu Lys Lys Glu Ala Ala Thr GlyVal Leu Thr Phe Phe Ser 1 5 10 15 Leu Asp Ser Met Ala Arg Asp Pro Val 2025 432 25 PRT Chlamydophila pneumoniae 432 Ala Lys Asp Lys Lys Glu AlaAla Ser Gly Val Met Thr Phe Phe Thr 1 5 10 15 Leu Gly Ala Met Asp ArgLys Asn Glu 20 25 433 25 PRT Nostoc punctiforme 433 Gln Ser Arg Ala LysAsp Arg Ala Ser Gly Gln Gly Asn Leu Phe Asp 1 5 10 15 Leu Leu Gly AspGly Phe Ser Ser Thr 20 25 434 25 PRT Anabaena sp. 434 Gln Ser Arg AlaArg Asp Arg Ala Ser Gly Gln Gly Asn Leu Phe Asp 1 5 10 15 Leu Leu GlyGly Tyr Ser Ser Thr Asn 20 25 435 25 PRT Synechocystis sp. 435 Gln LysArg Ala Lys Glu Lys Glu Thr Gly Gln Leu Asn Ile Phe Asp 1 5 10 15 SerLeu Thr Ala Gly Glu Ser Ile Lys 20 25 436 25 PRT Prochlorococcus marinus436 Ser Ser Arg Asn Arg Asp Arg Ile Ser Gly Gln Gly Asn Leu Phe Asp 1 510 15 Ser Ile Ser Lys Asn Asp Thr Lys Glu 20 25 437 25 PRTProchlorococcus marinus 437 Ala Ser Arg Ala Arg Asp Arg Leu Ser Gly GlnGly Asn Leu Phe Asp 1 5 10 15 Leu Val Ala Gly Ala Ala Asp Glu Gln 20 25438 25 PRT Synechococcus sp. 438 Ser Ser Arg Ala Lys Asp Arg Asp Ser GlyGln Gly Asn Leu Phe Asp 1 5 10 15 Leu Met Ala Ala Pro Asn Asp Glu Asp 2025 439 25 PRT Treponema denticola 439 Ser Gln Lys Lys Glu Asn Glu SerThr Gly Gln Gly Ser Leu Phe Glu 1 5 10 15 Gly Ser Gly Ile Lys Glu PheSer Asp 20 25 440 25 PRT Treponema pallidum 440 Ala Arg Lys Lys Ala ValThr Ser Ser Arg Gln Ala Ser Leu Phe Asp 1 5 10 15 Glu Thr Asp Leu GlyGlu Cys Ser Glu 20 25 441 25 PRT Borrelia burgdorferi 441 Ser Glu AspLys Asn Asn Lys Lys Leu Gly Gln Asn Ser Leu Phe Gly 1 5 10 15 Ala LeuGlu Ser Gln Asp Pro Ile Gln 20 25 442 25 PRT Magnetospirillummagnetotacticum 442 Ala Gln Ala Ala Glu Asp Arg Gln Ser Ser Gln Met SerLeu Leu Gly 1 5 10 15 Gly Ser Asn Ala Pro Thr Leu Lys Leu 20 25 443 25PRT Rhodopseudomonas palustris 443 Gln Arg Asn His Glu Ala Ala Thr SerGly Gln Asn Asp Met Phe Gly 1 5 10 15 Gly Leu Ser Asp Ala Pro Ser IleIle 20 25 444 25 PRT Mesorhizobium loti 444 Ser Leu Ala Gln Gln Asn AlaVal Ser Gly Gln Ala Asp Ile Phe Gly 1 5 10 15 Ala Ser Leu Gly Ala GlnSer Gln Ala 20 25 445 25 PRT Brucella suis 445 Gln Arg Thr Gln Glu AsnAla Val Ser Gly Gln Ser Asp Ile Phe Gly 1 5 10 15 Leu Ser Gly Ala ProArg Glu Thr Leu 20 25 446 25 PRT Sinorhizobium meliloti 446 Gln Arg AlaGln Glu Asn Lys Val Ser Gly Gln Ser Asp Met Phe Gly 1 5 10 15 Ala GlyAla Ala Thr Gly Pro Glu Lys 20 25 447 25 PRT Agrobacterium tumefaciens447 Gln Met Ala Gln Asn Asn Arg Thr Ile Gly Gln Ser Asp Met Phe Gly 1 510 15 Ser Gly Gly Gly Thr Gly Pro Glu Lys 20 25 448 25 PRT Caulobactercrescentus 448 Gln Ser Cys His Ala Asp Arg Gln Gly Gly Gln Gly Gly LeuPhe Gly 1 5 10 15 Ser Asp Pro Gly Ala Gly Arg Pro Arg 20 25 449 25 PRTRhodobacter sphaeroides 449 Ala Ala Ile His Glu Ala Leu Asn Ser Ser GlnVal Ser Leu Phe Gly 1 5 10 15 Glu Ala Gly Ala Asp Ile Pro Glu Pro 20 25450 25 PRT Rhodobacter capsulatus 450 Ala Ala Val Ala Glu Ala Lys SerSer Ala Gln Val Ser Leu Phe Gly 1 5 10 15 Glu Ala Gly Asp Asp Leu ProPro Arg 20 25 451 25 PRT Rickettsia conorii 451 Thr Ala Tyr His Glu GluGln Glu Ser Asn Gln Phe Ser Leu Ile Lys 1 5 10 15 Val Ser Ser Leu SerPro Thr Ile Leu 20 25 452 25 PRT Rickettsia helvetica 452 Thr Ser TyrHis Glu Glu Gln Glu Ser Asn Gln Leu Ser Leu Ile Lys 1 5 10 15 Val SerSer Leu Ser Pro Thr Ile Leu 20 25 453 25 PRT Rickettsia prowazekii 453Thr Ser Tyr His Gln Glu Gln Glu Ser Asn Gln Phe Ser Leu Ile Lys 1 5 1015 Val Ser Ser Leu Ser Pro Thr Ile Leu 20 25 454 25 PRT Rickettsiarickettsii 454 Thr Ala Tyr His Glu Glu Gln Glu Ser Asn Gln Phe Ser LeuIle Lys 1 5 10 15 Val Ser Ser Leu Ser Pro Thr Ile Leu 20 25 455 25 PRTCowdria ruminantium 455 Glu Tyr Asn Lys Tyr Asn Ser Ser Phe Asn Gln IleSer Leu Phe Asn 1 5 10 15 Asp Lys Asn His Tyr Lys Leu Val Glu 20 25 45625 PRT Wolbachia sp. 456 Asn Lys Asn Lys Gln Asp Lys Glu Ser Ser Gln AlaAla Leu Phe Gly 1 5 10 15 Ser Leu Asp Val Leu Lys Pro Lys Leu 20 25 45725 PRT Sphingomonas aromaticivorans 457 Glu Glu Ala Ser Arg Ser Arg ThrSer Gly Gln Gly Gly Leu Phe Gly 1 5 10 15 Gly Asp Asp His Ala Thr ProAla Thr 20 25 458 25 PRT Neisseria gonorrhoeae 458 Asn Ala Asp Gln LysAla Ala Asn Ala Asn Gln Gly Gly Leu Phe Asp 1 5 10 15 Met Met Glu AspAla Ile Glu Pro Val 20 25 459 25 PRT Neisseria meningitidis 459 Asn AlaAsp Gln Lys Ala Ala Asn Ala Asn Gln Gly Gly Leu Phe Asp 1 5 10 15 MetMet Glu Asp Ala Ile Glu Pro Val 20 25 460 25 PRT Nitrosomonas 460 TyrAla Glu Gln Cys Ser Leu Ala Ala Ser Gln Val Ser Leu Phe Asp 1 5 10 15Glu Asn Thr Asp Leu Ile Gln Pro Pro 20 25 461 25 PRT Bordetellabronchiseptica 461 Ala Ala Glu Gln Ala Ala Arg Ser Ala Asn Gln Ser SerLeu Phe Gly 1 5 10 15 Asp Asp Ser Gly Asp Val Val Ala Gly 20 25 462 25PRT Bordetella pertussis 462 Ala Ala Glu Gln Ala Ala Arg Ser Ala Asn GlnSer Ser Leu Phe Gly 1 5 10 15 Asp Asp Ser Gly Asp Val Val Ala Gly 20 25463 25 PRT Burkholderia pseudomallei 463 Ala Ala Glu Gln Ala Ala Ala AsnAla Leu Gln Ala Gly Leu Phe Asp 1 5 10 15 Ile Gly Gly Val Pro Ala HisGln His 20 25 464 25 PRT Burkholderia cepacia 464 Ala Ala Glu Gln AlaSer Ala Asn Ala Leu Gln Ala Gly Leu Phe Asp 1 5 10 15 Met Gly Asp AlaPro Ser Gln Gly His 20 25 465 25 PRT Burkholderia mallei 465 Ala Ala GluGln Ala Ala Ala Asn Ala Leu Gln Ala Gly Leu Phe Asp 1 5 10 15 Ile GlyGly Val Pro Ala His Gln His 20 25 466 25 PRT Ralstonia metallidurans 466Leu Asp Arg Thr Glu Gly Glu Ser Ala Asn Gln Val Ser Leu Phe Asp 1 5 1015 Leu Met Asp Asp Ala Gly Ala Ser His 20 25 467 25 PRTAcidothiobacillus ferrooxidans 467 Ala Gln Phe Gln Ser Ser Gln Ala SerLeu Gln Glu Ser Leu Phe Ser 1 5 10 15 Gly Gln Glu Ala Leu Arg Val AlaPro 20 25 468 25 PRT Xylella fastidiosa 468 Glu Gln Met Ser Arg Glu ArgGlu Ser Gly Gln Asn Pro Leu Phe Gly 1 5 10 15 Asn Ala Asp Pro Ser ThrPro Ala Ile 20 25 469 25 PRT Xylella fastidiosa 469 Glu Gln Met Ser ArgGlu Arg Glu Ser Gly Gln Asn Ser Leu Phe Gly 1 5 10 15 Asn Ala Asp ProGly Thr Pro Ala Ile 20 25 470 25 PRT Xylella fastidiosa 470 Glu Gln MetSer Arg Glu Arg Glu Ser Gly Gln Asn Ser Leu Phe Gly 1 5 10 15 Asn AlaAsp Pro Gly Thr Pro Ala Ile 20 25 471 25 PRT Legionella pneumophila 471Glu Lys Glu His Gln Asn Gln Ser Ser Gly Gln Phe Asp Leu Phe Ser 1 5 1015 Leu Leu Glu Asp Lys Ala Asp Glu Gln 20 25 472 25 PRT Coxiellaburnetii 472 Glu Gln Arg Asn Arg Asp Met Ile Leu Gly Gln His Asp Leu PheGly 1 5 10 15 Glu Glu Val Lys Gly Ile Asp Glu Asp 20 25 473 25 PRTMethylococcus capsulatus 473 Glu Gln Gln Gly Ala Met Ser Ala Ala Gly GlnAsp Asp Leu Phe Gly 1 5 10 15 Gly Phe Thr Ala Glu Ser Pro Ala Ala 20 25474 25 PRT Pseudomonas aeruginosa 474 Glu Gln Thr Ala Arg Ser His AspSer Gly His Met Asp Leu Phe Gly 1 5 10 15 Gly Val Phe Ala Glu Pro GluAla Asp 20 25 475 25 PRT Pseudomonas putida 475 Glu Gln Ala Ala His ThrAla Asp Ser Gly His Val Asp Leu Phe Gly 1 5 10 15 Ser Met Phe Asp AlaAla Asp Val Asp 20 25 476 25 PRT Pseudomonas syringae 476 Glu Gln ThrAla Arg Ser His Asp Ser Gly His Ser Asp Leu Phe Gly 1 5 10 15 Gly LeuPhe Val Glu Ala Asp Ala Asp 20 25 477 25 PRT Pseudomonas fluorescens 477Glu Gln Thr Ala Arg Thr Arg Asp Ser Gly His Ala Asp Leu Phe Gly 1 5 1015 Gly Leu Phe Val Glu Glu Asp Ala Asp 20 25 478 25 PRT Shewanellaputrefaciens 478 Asp Gln His Ala Lys Ala Glu Ala Ile Gly Gln His Asp MetPhe Gly 1 5 10 15 Leu Leu Asn Ser Asp Pro Glu Asp Ser 20 25 479 25 PRTVibrio cholerae 479 Ser Gln His His Gln Ala Glu Ala Phe Gly Gln Ala AspMet Phe Gly 1 5 10 15 Val Leu Thr Asp Ala Pro Glu Glu Val 20 25 480 25PRT Pasteurella multocida 480 Asp Gln His Ala Lys Asp Ala Ala Met GlyGln Ala Asp Met Phe Gly 1 5 10 15 Val Leu Thr Glu Ser His Glu Asp Val 2025 481 25 PRT Haemophilus influenzae 481 Asp Gln His Ala Lys Asp Glu AlaMet Gly Gln Thr Asp Met Phe Gly 1 5 10 15 Val Leu Thr Glu Thr His GluAsp Val 20 25 482 25 PRT Haemophilus ducreyi 482 Asp Gln His Ser Lys MetGlu Ala Leu Gly Gln Ser Asp Met Phe Gly 1 5 10 15 Val Leu Thr Glu ThrPro Glu Gln Val 20 25 483 25 PRT Actinobacillus actinomycetemcomitans483 Asp Gln His Ala Lys Asp Glu Ala Leu Gly Gln Val Asp Met Phe Gly 1 510 15 Val Leu Thr Glu Thr Asn Glu Glu Val 20 25 484 25 PRT Buchnera sp.484 Lys Glu Ser Phe Arg Ile Lys Ser Phe Lys Gln Asp Ser Leu Phe Gly 1 510 15 Ile Phe Gln Asn Glu Leu Asn Gln Val 20 25 485 25 PRT Escherichiacoli 485 Asp Gln His Ala Lys Ala Glu Ala Ile Gly Gln Ala Asp Met Phe Gly1 5 10 15 Val Leu Ala Glu Glu Pro Glu Gln Ile 20 25 486 25 PRTSalmonella typhi 486 Asp Gln His Ala Lys Ala Glu Ala Ile Gly Gln Thr AspMet Phe Gly 1 5 10 15 Val Leu Ala Glu Glu Pro Glu Gln Ile 20 25 487 25PRT Salmonella typhimurium 487 Asp Gln His Ala Lys Ala Glu Ala Ile GlyGln Thr Asp Met Phe Gly 1 5 10 15 Val Leu Ala Glu Glu Pro Glu Gln Ile 2025 488 25 PRT Yersinia pestis 488 Asp Gln His Ala Lys Ala Glu Ala IleGly Gln Val Asp Met Phe Gly 1 5 10 15 Val Leu Ala Asp Ala Pro Glu GlnVal 20 25 489 25 PRT Desulfovibrio vulgaris 489 Gln Lys Lys Leu Lys GluArg Asp Ser Asn Gln Val Ser Leu Phe Thr 1 5 10 15 Met Ile Lys Glu GluPro Lys Val Cys 20 25 490 25 PRT Geobacter sulfurreducens 490 Gln LysIle Gln Gln Glu Lys Glu Ser Ala Gln Val Ser Leu Phe Gly 1 5 10 15 AlaGlu Glu Ile Val Arg Thr Asn Gly 20 25 491 25 PRT Helicobacter pylori 491Lys Asp Lys Ala Asn Glu Met Met Gln Gly Gly Asn Ser Leu Phe Gly 1 5 1015 Ala Met Glu Gly Gly Ile Lys Glu Gln 20 25 492 25 PRT Campylobacterjejuni 492 Arg Lys Met Ala Glu Val Arg Lys Asn Ala Ala Ser Ser Leu PheGly 1 5 10 15 Glu Glu Glu Leu Thr Ser Gly Val Gln 20 25 493 25 PRTStreptomyces coelicolor 493 Val Ala Val Lys Arg Lys Glu Ala Glu Gly GlnPhe Asp Leu Phe Gly 1 5 10 15 Gly Met Gly Asp Glu Gln Ser Asp Glu 20 25494 25 PRT Saccharopolyspora erythraea 494 Ile Gly Leu Lys Arg Gln GlnAla Leu Gly Gln Phe Asp Leu Phe Gly 1 5 10 15 Gly Gly Asp Asp Ala GlyGly Glu Glu 20 25 495 25 PRT Thermobifida fusca 495 Leu Ser Ser Lys LysGln Glu Ala His Gly Gln Phe Asp Leu Phe Gly 1 5 10 15 Gly Gly Asp GluGlu Asp Gly Gly Glu 20 25 496 25 PRT Mycobacterium avium 496 Leu Gly ThrLys Lys Ala Glu Ala Met Gly Gln Phe Asp Leu Phe Gly 1 5 10 15 Gly AspGly Gly Cys Thr Glu Ser Val 20 25 497 25 PRT Mycobacterium leprae 497Leu Gly Thr Lys Lys Ala Glu Ala Ile Gly Gln Phe Asp Leu Phe Gly 1 5 1015 Gly Thr Asp Gly Thr Asp Ala Val Phe 20 25 498 25 PRT Mycobacteriumsmegmatis 498 Leu Gly Thr Lys Lys Ala Glu Ala Met Gly Gln Phe Asp LeuPhe Gly 1 5 10 15 Gly Gly Glu Asp Thr Gly Thr Asp Ala 20 25 499 25 PRTMycobacterium tuberculosis 499 Leu Gly Thr Lys Lys Ala Glu Ala Leu GlyGln Phe Asp Leu Phe Gly 1 5 10 15 Ser Asn Asp Asp Gly Thr Gly Thr Ala 2025 500 25 PRT Corynebacterium diptheriae 500 Thr Ser Thr Lys Lys Ala AlaAsp Lys Gly Gln Phe Asp Leu Phe Ala 1 5 10 15 Gly Leu Gly Ala Asp AlaGlu Glu Val 20 25 501 25 PRT Dehalococcoides ethenogenes 501 Gln Arg GluGln Lys Leu Lys Asp Ser Asn Gln Thr Thr Met Phe Asp 1 5 10 15 Leu PheGly Gln Gln Ser Pro Met Pro 20 25 502 25 PRT Clostridium difficile 502Ser Met Asp Arg Lys Lys Asn Val Gln Gly Gln Ile Ser Leu Phe Asp 1 5 1015 Ala Phe Gly Asp Ser Glu Glu Asp Ser 20 25 503 25 PRT Carboxydothermushydrogenoformans 503 Glu Phe Tyr Ser Lys Lys Ser Asn Gly Val Gln Leu ThrLeu Gly Asp 1 5 10 15 Phe Leu Pro Glu Ala Asp Arg Tyr Asn 20 25 504 25PRT Bacillus halodurans 504 Ala Glu Gln Val Lys Glu Phe Gln Glu Asn ThrGly Gly Leu Phe Gln 1 5 10 15 Leu Ser Val Glu Glu Pro Glu Tyr Ile 20 25505 25 PRT Bacillus stearothermophilus 505 Ile Ala Ile Glu His Ala GlnTrp Val Gln Ala Leu Glu Ala Gly Gly 1 5 10 15 Leu Ser Leu Lys Pro LysTyr Ala Ala 20 25 506 25 PRT Bacillus subtilis 506 His Ala Glu Leu PheAla Ala Asp Asp Asp Gln Met Gly Leu Phe Leu 1 5 10 15 Asp Glu Ser PheSer Ile Lys Pro Lys 20 25 507 25 PRT Staphylococcus aureus 507 Val LeuAsp Gly Asp Leu Asn Ile Glu Gln Asp Gly Phe Leu Phe Asp 1 5 10 15 IleLeu Thr Pro Lys Gln Met Tyr Glu 20 25 508 25 PRT Staphylococcusepidermidis 508 Val Leu Asp Leu Asn Ser Asp Val Glu Gln Asp Glu Met LeuPhe Asp 1 5 10 15 Leu Leu Thr Pro Lys Gln Ser Tyr Glu 20 25 509 25 PRTBacillus anthracis 509 Leu Lys Gly Ala Leu Glu Tyr Ala Asn Leu Ala ArgAsp Leu Gly Asp 1 5 10 15 Ala Val Pro Lys Ser Lys Tyr Val Gln 20 25 51025 PRT Listeria innocua 510 Tyr Ile Ser Leu Leu Gly Glu Asp Ser Lys GlyMet Asn Leu Phe Ala 1 5 10 15 Glu Asp Asp Asp Phe Leu Lys Lys Met 20 25511 25 PRT Listeria monocytogenes 511 Tyr Ile Ser Leu Leu Gly Glu AspSer Lys Gly Met Asn Leu Phe Ala 1 5 10 15 Glu Asp Asp Asp Phe Leu LysLys Met 20 25 512 25 PRT Listeria monocytogenes 512 Tyr Ile Ser Leu LeuGly Glu Asp Ser Lys Gly Met Asn Leu Phe Ala 1 5 10 15 Glu Asp Asp GluPhe Leu Lys Lys Met 20 25 513 25 PRT Enterococcus faecalis 513 Asn IleGln Ser Ile Leu Leu Ser Gly Gly Ser Met Asp Leu Leu Glu 1 5 10 15 ThrLeu Pro Lys Glu Glu Glu Ile Ala 20 25 514 25 PRT Enterococcus faecium514 Lys Ile Gln Asn Ile Val Tyr Ser Gly Gly Ser Leu Asp Leu Leu Gly 1 510 15 Ile Met Ala Leu Lys Glu Glu Glu Val 20 25 515 25 PRT Lactococcuslactis 515 Ala Asp His Ala Asn Leu Leu Asn Tyr Tyr Ser Asp Asp Ile PheMet 1 5 10 15 Ala Ser Ser Gly Gly Gly Phe Ala Tyr 20 25 516 25 PRTStreptococcus equi 516 Leu Glu Gly Leu Leu Thr Phe Val Asn Glu Leu GlySer Leu Phe Ala 1 5 10 15 Asp Ser Ser Phe Ser Trp Val Glu Thr 20 25 51725 PRT Streptococcus pyogenes 517 Leu Asp Gly Leu Leu Val Phe Val AsnGlu Leu Gly Ser Leu Phe Ser 1 5 10 15 Asp Ser Ser Phe Ser Trp Val AspThr 20 25 518 25 PRT Streptococcus mutans 518 Leu Glu His Leu Phe ThrPhe Val Asn Glu Leu Gly Ser Leu Phe Ala 1 5 10 15 Asp Ser Ser Tyr AsnTrp Ile Glu Ala 20 25 519 25 PRT Streptococcus pneumoniae 519 Leu AlaAsn Leu Phe Glu Phe Val Lys Glu Leu Gly Ser Leu Phe Gly 1 5 10 15 AspAla Ile Tyr Ser Trp Gln Glu Ser 20 25 520 25 PRT Ureaplasma urealyticum520 Glu Lys Thr Gly Leu Asn Gly His Phe Phe Asp Leu Asn Leu Val Gly 1 510 15 Leu Asp Tyr Ala Lys Asp Met Ser Val 20 25 521 25 PRT Mycoplasmagenitalium 521 Asn Asp Ala Lys Asp Phe Trp Ile Lys Ser Asp His Leu LeuPhe Thr 1 5 10 15 Arg Met Pro Leu Glu Lys Lys Asp Ser 20 25 522 25 PRTMycoplasma pneumoniae 522 Asn Leu Ala Lys Ser Phe Trp Val Gln Ser AsnHis Glu Leu Phe Pro 1 5 10 15 Lys Ile Pro Leu Asp Gln Pro Pro Val 20 25523 25 PRT Mycoplasma pulmonis 523 Leu Ala Lys Val Gln Gly Asp Asp IleAsp Ile Ser Asn Phe Phe Gln 1 5 10 15 Leu Glu Phe Ser Lys Asn Ser SerArg 20 25 524 25 PRT Clostridium acetobutylicum 524 Ser Gly Gln Arg LysLys Asn Leu Lys Gly Gln Met Asn Leu Phe Thr 1 5 10 15 Asp Phe Val GlnAsp Asp Tyr Glu Glu 20 25 525 25 PRT Rhodopseudomonas palustris 525 TrpAla Val Arg Arg Leu Pro Asp Asp Val Pro Leu Pro Leu Phe Glu 1 5 10 15Ala Ala Ser Ala Arg Glu Gln Glu Asp 20 25 526 25 PRT Mesorhizobium loti526 Arg Ala Leu Gly Ala Lys Ser Ala Ala Glu Lys Leu Pro Leu Phe Asp 1 510 15 Gln Pro Ala Leu Arg Leu Arg Glu Leu 20 25 527 25 PRT Brucella suis527 Trp Ala Val Arg Arg Leu Pro Asn Asp Glu Thr Leu Pro Leu Pro Arg 1 510 15 Ala Ala Ala Ala Ser Glu Leu Ala Gln 20 25 528 25 PRT Sinorhizobiummeliloti 528 Lys Ala Leu Asp Glu Gln Ser Ala Val Glu Arg Leu Pro Leu PheGlu 1 5 10 15 Gly Ala Gly Ser Asp Asp Leu Gln Ile 20 25 529 25 PRTSinorhizobium meliloti 529 Leu Trp Ala Ile Lys Ala Leu Arg Asp Glu ProLeu Pro Leu Phe Thr 1 5 10 15 Ala Ala Ala Asp Arg Glu Ala Arg Ala 20 25530 25 PRT Agrobacterium tumefaciens 530 Leu Trp Ala Ile Lys Ala Leu ArgAsp Glu Pro Leu Pro Leu Phe Ala 1 5 10 15 Ala Ala Ala Ile Arg Glu AsnAla Val 20 25 531 25 PRT Agrobacterium tumefaciens 531 Leu Trp Ala IleLys Ala Leu Arg Asp Glu Pro Leu Pro Leu Phe Ala 1 5 10 15 Ala Ala AlaGlu Arg Glu Ala Thr Ala 20 25 532 25 PRT Agrobacterium tumefaciens 532Leu Trp Ala Ile Lys Ala Leu Arg Asp Glu Pro Leu Pro Leu Phe Ala 1 5 1015 Ala Ala Ala Glu Arg Glu Met Ala Ala 20 25 533 25 PRT Caulobactercrescentus 533 Gly Leu Lys Gly Glu His Lys Ala Pro Val Gln Ala Pro LeuLeu Ala 1 5 10 15 Gly Leu Pro Leu Phe Glu Glu Arg Val 20 25 534 25 PRTRhodobacter capsulatus 534 Trp Ala Val Arg Ala Ile Arg Ala Pro Lys ProLeu Pro Leu Phe Ala 1 5 10 15 Asn Pro Leu Asp Gly Glu Gly Gly Ile 20 25535 25 PRT Sphingomonas aromaticivorans 535 Leu Trp Asp Val Arg Arg ThrPro Pro Thr Gln Leu Pro Leu Phe Ala 1 5 10 15 Phe Ala Asn Ala Pro GluLeu Gly Gln 20 25 536 24 PRT Bordetella bronchiseptica 536 Ala Trp GlnAla Ala Ala Ser Ala Gln Ser Arg Asp Leu Leu Arg Glu 1 5 10 15 Ala ValIle Val Glu Thr Glu Thr 20 537 25 PRT Bordetella parapertussis 537 AlaSer Trp Gln Ala Ala Ala Ser Ala Gln Ser Arg Asp Leu Leu Arg 1 5 10 15Glu Ala Val Ile Val Glu Thr Glu Thr 20 25 538 25 PRT Bordetellapertussis 538 Ala Ser Trp Gln Ala Ala Ala Ser Ala Gln Ser Arg Asp LeuLeu Arg 1 5 10 15 Glu Ala Val Ile Val Glu Thr Glu Thr 20 25 539 25 PRTBurkholderia pseudomallei 539 Ala Leu Trp Gln Ala Val Ala Ala Ala ProGlu Arg Gly Leu Leu Ala 1 5 10 15 Ala Ala Pro Ile Asp Glu Ala Val Arg 2025 540 25 PRT Burkholderia cepacia 540 Arg Trp Trp Ala Val Thr Ala GlnHis Ala Val Pro Arg Leu Leu Arg 1 5 10 15 Asp Ala Pro Ile Ala Glu AlaAla Leu 20 25 541 25 PRT Ralstonia metallidurans 541 His Ala Arg Gly AlaAla Val Gln Thr Gln His Arg Asp Leu Leu His 1 5 10 15 Asp Ala Pro ProGln Glu His Ala Leu 20 25 542 25 PRT Acidothiobacillus ferrooxidans 542Arg His Gln Ala Leu Trp Ala Val Gln Gly Ser Leu Pro Leu Pro Thr 1 5 1015 Ala Leu Pro Met Pro Val Val Pro Glu 20 25 543 25 PRT Methylococcuscapsulatus 543 Ala Phe Trp Glu Ala Ala Gly Val Glu Ala Pro Thr Pro LeuTyr Ala 1 5 10 15 Glu Pro Gln Phe Ala Glu Ala Glu Pro 20 25 544 25 PRTPseudomonas aeruginosa 544 Ala Arg Trp Ala Val Ala Ser Val Glu Pro GlnLeu Pro Leu Phe Ala 1 5 10 15 Glu Gly Thr Ala Ile Glu Glu Ser Thr 20 25545 25 PRT Pseudomonas putida 545 Ala Arg Trp Gln Val Ala Ala Val GlnPro Gln Leu Pro Leu Phe Ala 1 5 10 15 Asp Val Gln Ala Leu Pro Glu GluPro 20 25 546 25 PRT Pseudomonas syringae 546 Ala Arg Trp Glu Val AlaGly Val Glu Ala Gln Arg Pro Leu Phe Asp 1 5 10 15 Asp Val Thr Ser GluGlu Val Gln Val 20 25 547 25 PRT Pseudomonas fluorescens 547 Ala Arg TrpGlu Val Ala Gly Val Gln Lys Gln Leu Gly Leu Phe Ala 1 5 10 15 Gly LeuPro Ser Gln Glu Glu Pro Asp 20 25 548 25 PRT Mycobacterium avium 548 AlaGly Ala Ala Ala Thr Gln Arg Pro Asp Arg Leu Pro Gly Val Gly 1 5 10 15Ser Ser Ser His Ile Pro Ala Leu Pro 20 25 549 18 PRT Mycobacteriumleprae 549 Arg Ala Asn Arg Leu Pro Gly Val Gly Gly Ser Ser His Ile ProVal 1 5 10 15 Leu Pro 550 25 PRT Mycobacterium smegmatis 550 Ala Gly AlaAla Ala Thr Gln Arg Pro Asp Arg Leu Pro Gly Val Gly 1 5 10 15 Ser SerThr His Ile Pro Pro Leu Pro 20 25 551 25 PRT Mycobacterium tuberculosis551 Ala Gly Ala Ala Ala Thr Gly Arg Pro Asp Arg Leu Pro Gly Val Gly 1 510 15 Ser Ser Ser His Ile Pro Ala Leu Pro 20 25 552 25 PRTCorynebacterium diptheriae 552 Ala Gly Ala Ala Ala Thr Glu Lys Ala AlaMet Leu Pro Gly Leu Ser 1 5 10 15 Met Val Ser Ala Pro Ser Leu Pro Gly 2025 553 15 PRT Thermotoga maritima 553 Gly Val Leu Gly Asp Leu Pro GluThr Glu Gln Phe Thr Leu Phe 1 5 10 15 554 19 PRT Desulfitobacteriumhafniense 554 Asp Cys Leu Lys Gly Ile Pro Glu Ser Asp Gln Ile Ser PhePhe Asp 1 5 10 15 Leu Ile Ser 555 15 PRT Clostridium difficile 555 GlySer Leu Glu Asn Met Ser Glu Arg Asn Gln Leu Ser Leu Phe 1 5 10 15 556 16PRT Carboxydothermus hydrogenoformans 556 Gly Cys Leu Lys Gly Leu AlaPro Thr Ser Gln Leu Val Leu Phe Ala 1 5 10 15 557 15 PRT Bacillushalodurans 557 Gly Cys Leu Glu Gly Leu Pro Glu Ser Asn Gln Leu Ser LeuPhe 1 5 10 15 558 15 PRT Bacillus stearothermophilus 558 Gly Cys Leu AspSer Leu Pro Asp His Asn Gln Leu Ser Leu Phe 1 5 10 15 559 15 PRTBacillus subtilis 559 Gly Cys Leu Glu Ser Leu Pro Asp Gln Asn Gln LeuSer Leu Phe 1 5 10 15 560 17 PRT Staphylococcus aureus 560 Gly Ser LeuPro Asn Leu Pro Asp Lys Ala Gln Leu Ser Ile Phe Asp 1 5 10 15 Met 561 17PRT Staphylococcus epidermidis 561 Gly Ser Leu Pro Asp Leu Pro Asp LysAla Gln Leu Ser Ile Phe Asp 1 5 10 15 Met 562 15 PRT Bacillus anthracis562 Gly Cys Leu Gly Asp Leu Pro Asp Gln Asn Gln Leu Ser Leu Phe 1 5 1015 563 15 PRT Listeria innocua 563 Gly Cys Leu Glu Gly Leu Pro Asp GlnAsn Gln Leu Ser Leu Phe 1 5 10 15 564 15 PRT Listeria monocytogenes 564Gly Cys Leu Glu Gly Leu Pro Asp Gln Asn Gln Leu Ser Leu Phe 1 5 10 15565 15 PRT Listeria monocytogenes 565 Gly Cys Leu Glu Gly Leu Pro AspGln Asn Gln Leu Ser Leu Phe 1 5 10 15 566 18 PRT Enterococcus faecalis566 Gly Val Leu Lys Asp Leu Pro Asp Glu Asn Gln Leu Ser Leu Phe Asp 1 510 15 Met Leu 567 15 PRT Enterococcus faecium 567 Gly Val Leu Lys AspLeu Pro Asp Glu Asn Gln Leu Ser Leu Phe 1 5 10 15 568 19 PRT Lactococcuslactis 568 Gly Val Leu Glu Gly Met Pro Asp Asp Asn Gln Leu Ser Leu PheAsp 1 5 10 15 Asp Phe Phe 569 19 PRT Streptococcus equi 569 Gly Ile LeuGly Asn Met Pro Asp Asp Asn Gln Leu Ser Leu Phe Asp 1 5 10 15 Asp PhePhe 570 19 PRT Streptococcus pyogenes 570 Gly Ile Leu Gly Asn Met ProGlu Asp Asn Gln Leu Ser Leu Phe Asp 1 5 10 15 Asp Phe Phe 571 19 PRTStreptococcus mutans 571 Gly Ile Leu Gly Ser Met Pro Glu Asp Asn Gln LeuSer Leu Phe Asp 1 5 10 15 Asp Phe Phe 572 19 PRT Streptococcusthermophilus 572 Gly Ile Leu Gly Asn Met Pro Glu Asp Asn Gln Leu Ser LeuPhe Asp 1 5 10 15 Asp Phe Phe 573 19 PRT Streptococcus pneumoniae 573Gly Ile Leu Gly Asn Met Pro Glu Asp Asn Gln Leu Ser Leu Phe Asp 1 5 1015 Glu Leu Phe 574 15 PRT Ureaplasma urealyticum 574 Gly Val Leu Asp HisLeu Ser Glu Thr Glu Gln Leu Thr Leu Phe 1 5 10 15 575 16 PRT Mycoplasmagenitalium 575 Gln Leu Phe Asp Glu Phe Glu His Gln Asp Asp His Lys LeuPhe Asn 1 5 10 15 576 15 PRT Mycoplasma pneumoniae 576 Leu Leu Asp GluPhe Arg Glu Gln Asp Asn Gln Lys Lys Leu Phe 1 5 10 15 577 15 PRTMycoplasma pulmonis 577 Gly Ile Phe Glu Gln Ile Pro Glu Thr Asn Gln IlePhe Leu Ile 1 5 10 15 578 18 PRT Clostridium acetobutylicum 578 Gly CysLeu Lys Gly Leu Pro Glu Ser Asp Gln Leu Ser Phe Phe Asp 1 5 10 15 AlaIle 579 25 PRT Acidothiobacillus ferrooxidans 579 Pro Val Ser Asp ThrAla Phe Ala Gly Trp Gln Leu Ser Leu Phe Gln 1 5 10 15 Gly Phe Leu AlaAsn Thr Asp Asp Gln 20 25 580 14 PRT Buchnera aphidicola 580 Met Leu LeuPhe Lys Ile Leu Gln Ser Lys Phe Lys Lys Asp 1 5 10 581 25 PRTEscherichia coli 581 Glu Lys Leu Asp Val Ile Lys Asp Ser Pro Gln Met SerLeu Phe Glu 1 5 10 15 Ile Ile Glu Ser Pro Ala Lys Lys Asp 20 25 582 30DNA Artificial Sequence synthetic oligonucleotide primer 582 tggctggaattcaaatttac cgtagaacgt 30 583 30 DNA Artificial Sequence syntheticoligonucleotide primer 583 agtccagaat tcttacagtc tcattggcat 30 584 32DNA Artificial Sequence synthetic oligonucleotide primer 584 tttgatgaattcaaaagcga cgttgaatac gc 32 585 32 DNA Artificial Sequence syntheticoligonucleotide primer 585 gctttggaat tcgtgtcata tcaaacgtta tg 32 586 40DNA Artificial Sequence synthetic oligonucleotide primer 586 gactttgaattctcgagtta accacgttct gtcgggtgca 40 587 32 DNA Artificial Sequencesynthetic oligonucleotide primer 587 tttgatgaat tcaaaagcga cgttgaatac gc32 588 40 DNA Artificial Sequence synthetic oligonucleotide primer 588gactttgaat tctcgagtta cataacgttt gataagtcac 40 589 29 DNA ArtificialSequence synthetic oligonucleotide primer 589 gtcaggccga taaaaagggcgtgctggcc 29 590 29 DNA Artificial Sequence synthetic oligonucleotideprimer 590 gccagcacgc cctttttatc ggcctgacc 29 591 39 DNA ArtificialSequence synthetic oligonucleotide primer 591 gaagctatcg gtcctgccgatatgccaggc gtgctggcc 39 592 39 DNA Artificial Sequence syntheticoligonucleotide primer 592 ggccagcacg cctggcatat cggcaccacc gatagcttc 39593 35 DNA Artificial Sequence synthetic oligonucleotide primer 593ggaaagaatt cggtccggcg gcagatcaac acgcg 35 594 45 DNA Artificial Sequencesynthetic oligonucleotide primer 594 gatcaactcg agaggacctc cagctcccggctcttcggcc agcac 45 595 43 DNA Artificial Sequence syntheticoligonucleotide primer 595 tctcaaagaa ttcgcagcgg gtgcgagtca gggagtcgcgcag 43 596 36 DNA Artificial Sequence synthetic oligonucleotide primer596 aatccactcg aggcctccac cgatagcttc cgcttt 36 597 40 DNA ArtificialSequence synthetic oligonucleotide primer 597 tctcaaagaa ttcgcgggtgcgagtcaggg agtcgcgcag 40 598 33 DNA Artificial Sequence syntheticoligonucleotide primer 598 aatccactcg agtcccggtg cgttgtcatc gaa 33 59940 DNA Artificial Sequence synthetic oligonucleotide primer 599tctcaaagaa ttcgcgggtg cgccgcaaat ggaaagacaa 40 600 39 DNA ArtificialSequence synthetic oligonucleotide primer 600 aatccactcg agtccagctcctaatcccag caccagttg 39 601 26 DNA Artificial Sequence syntheticoligonucleotide primer 601 tctcaaagcc gccgctacgc aagtgg 26 602 40 DNAArtificial Sequence synthetic oligonucleotide primer 602 aatccactcgagtccagctc ctggtactga cagcaaagac 40 603 30 DNA Artificial Sequencesynthetic oligonucleotide primer 603 gggaattcca tatgttcgag gcgcgcctgg 30604 35 DNA Artificial Sequence synthetic oligonucleotide primer 604cgaagctttg cggccgccag tctcattggc atgac 35 605 30 DNA Artificial Sequencesynthetic oligonucleotide primer 605 gggaattccc atatgtatcg taaagatttg 30606 39 DNA Artificial Sequence synthetic oligonucleotide primer 606ccgctcgagt gcggccgcgg ggttaatgat tttttgaat 39 607 32 DNA ArtificialSequence synthetic oligonucleotide primer 607 gggaattcca tatgaaaaactccaaccgcc tt 32 608 39 DNA Artificial Sequence syntheticoligonucleotide primer 608 ccgctcgagt gcggccgctg gcgttttctt tttggataa 39609 26 DNA Artificial Sequence synthetic oligonucleotide primer 609gggaattcca tatggaaatc agtgtt 26 610 35 DNA Artificial Sequence syntheticoligonucleotide primer 610 cgaagctttg cggccgctta tagtgtgatt ggcat 35 61127 DNA Artificial Sequence synthetic oligonucleotide primer 611ggcatacata tgaaatttac cgtagaa 27 612 35 DNA Artificial Sequencesynthetic oligonucleotide primer 612 ctcgagtgcg gccgcttaca gtcttattggcatga 35 613 30 DNA Artificial Sequence synthetic oligonucleotide primer613 ctggaattct atcgtaaaga tttggaccat 30 614 39 DNA Artificial Sequencesynthetic oligonucleotide primer 614 ccgctcgagt gcggccgcgg ggttaatgattttttgaat 39 615 30 DNA Artificial Sequence synthetic oligonucleotideprimer 615 ctggaattca aaaactccaa ccgccttatt 30 616 39 DNA ArtificialSequence synthetic oligonucleotide primer 616 ccgctcgagt gcggccgctggcgttttctt tttggataa 39 617 37 DNA Artificial Sequence syntheticoligonucleotide primer 617 cactaaaggg cggccgcatg aaagcgttaa cggccag 37618 30 DNA Artificial Sequence synthetic oligonucleotide primer 618cgcctcgaga tgcaagtttt agcgttaaaa 30 619 36 DNA Artificial Sequencesynthetic oligonucleotide primer 619 cgaggagcct cgagtcataa caattccacgcttttg 36 620 34 DNA Artificial Sequence synthetic oligonucleotideprimer 620 gccaggctat gagtgcggct gccagtcgac aaac 34 621 34 DNAArtificial Sequence synthetic oligonucleotide primer 621 gtttgtcgactggcagccgc actcatagcc tggc 34 622 5 PRT Artificial Sequence syntheticpeptide 622 Gln Leu Ser Leu Phe 1 5 623 5 PRT Artificial Sequencesynthetic peptide 623 Gln Leu Ser Met Phe 1 5 624 5 PRT ArtificialSequence synthetic peptide 624 Gln Leu Asp Met Phe 1 5 625 5 PRTArtificial Sequence synthetic peptide 625 Gln Leu Asp Leu Phe 1 5 626 5PRT Artificial Sequence synthetic peptide 626 His Leu Ser Leu Phe 1 5627 5 PRT Artificial Sequence synthetic peptide 627 His Leu Ser Met Phe1 5 628 5 PRT Artificial Sequence synthetic peptide 628 His Leu Asp MetPhe 1 5 629 5 PRT Artificial Sequence synthetic peptide 629 His Leu AspLeu Phe 1 5 630 5 PRT Artificial Sequence synthetic peptide 630 Gln LeuAsn Leu Phe 1 5 631 5 PRT Escherichia coli 631 Gln Ala Asp Met Phe 1 5632 5 PRT Artificial Sequence synthetic peptide 632 Gln Ala Asp Lys Lys1 5 633 5 PRT Escherichia coli 633 Pro Ala Asp Met Pro 1 5 634 24 PRTEscherichia coli 634 Ala Ala Asp Gln His Ala Lys Ala Glu Ala Ile Gly GlnAla Asp Met 1 5 10 15 Phe Gly Val Leu Ala Glu Glu Pro 20 635 24 PRTEscherichia coli 635 Ala Ala Leu Met Asn Ser Leu Gly Ala Asp Leu Lys AlaAla Asp Gln 1 5 10 15 His Ala Lys Ala Glu Ala Ile Gly 20 636 5 PRTEscherichia coli 636 Gln Leu Gly Leu Phe 1 5 637 15 PRT Escherichia coli637 Ser Gln Gly Val Ala Gln Leu Asn Leu Phe Asp Asp Asn Ala Pro 1 5 1015 638 17 PRT Escherichia coli 638 Ala Ala Ala Thr Gln Val Asp Gly ThrGln Met Ser Leu Leu Ser Val 1 5 10 15 Pro 639 11 PRT Escherichia coli639 Pro Gln Met Glu Arg Gln Leu Val Leu Gly Leu 1 5 10 640 9 PRTEscherichia coli 640 Ile Gly Gln Ala Asp Met Phe Gly Val 1 5 641 9 PRTArtificial Sequence synthetic peptide 641 Ile Gly Gln Leu Asp Met PheGly Val 1 5 642 9 PRT Artificial Sequence synthetic peptide 642 Ile GlyGln Ala Ser Met Phe Gly Val 1 5 643 9 PRT Artificial Sequence syntheticpeptide 643 Ile Gly Gln Ala Asp Ala Phe Gly Val 1 5 644 9 PRTEscherichia coli 644 Ile Gly Gln Ala Asp Met Ala Gly Val 1 5 645 9 PRTArtificial Sequence synthetic peptide 645 Ile Gly Gln Ala Val Met PheGly Val 1 5 646 9 PRT Artificial Sequence synthetic peptide 646 Ile GlyPro Ala Asp Met Phe Gly Val 1 5 647 9 PRT Artificial Sequence syntheticpeptide 647 Ile Gly Lys Ala Asp Met Phe Gly Val 1 5 648 9 PRT ArtificialSequence synthetic peptide 648 Ile Gly Gln Ala Asp Lys Phe Gly Val 1 5649 9 PRT Artificial Sequence synthetic peptide 649 Ile Gly Gln Ala AspMet Lys Gly Val 1 5 650 9 PRT Artificial Sequence synthetic peptide 650Ile Gly Gln Ala Ala Met Phe Gly Val 1 5 651 9 PRT Artificial Sequencesynthetic peptide 651 Ile Gly Ala Ala Asp Met Phe Gly Val 1 5 652 9 PRTArtificial Sequence synthetic peptide 652 Ile Gly Gln Leu Ser Leu PheGly Val 1 5 653 9 PRT Artificial Sequence synthetic peptide 653 Ile GlyGln Leu Asp Leu Phe Gly Val 1 5 654 10 PRT Artificial Sequence syntheticpeptide 654 Ile Gly Gln Ala Met Ser Leu Phe Gly Val 1 5 10 655 10 PRTArtificial Sequence synthetic peptide 655 Ile Gly Gln Leu Val Leu GlyLeu Gly Val 1 5 10 656 10 PRT Artificial Sequence synthetic peptide 656Ile Gly Gln Leu Ser Leu Pro Leu Gly Val 1 5 10 657 8 PRT ArtificialSequence synthetic peptide 657 Ile Gly Leu Asn Leu Phe Gly Val 1 5 658 9PRT Artificial Sequence synthetic peptide 658 Ile Gly Gln Met Ser LeuLeu Gly Val 1 5 659 9 PRT Artificial Sequence synthetic peptide 659 IleGly Gln Leu Gly Leu Phe Gly Val 1 5 660 10 PRT Escherichia coli 660 ProAla Gln Leu Ser Leu Pro Leu Tyr Leu 1 5 10 661 9 PRT Escherichia coli661 Glu Ala Gln Leu Asp Leu Phe Asp Ser 1 5 662 5 PRT ArtificialSequence synthetic peptide 662 Gln Leu Asp Leu Phe 1 5 663 9 PRTArtificial Sequence synthetic peptide 663 Ile Gly Gln Leu Asp Leu PheGly Val 1 5 664 180 PRT Artificial Sequence truncated E. coli tauprotein 664 His His Ala Tyr Leu Phe Ser Gly Thr Arg Gly Val Gly Lys ThrSer 1 5 10 15 Ile Ala Arg Leu Leu Ala Lys Gly Leu Phe Val Asp Leu IleGlu Ile 20 25 30 Asp Ala Ala Arg Asp Leu Leu Asp Asn Val Gln Tyr Ala ProAla Arg 35 40 45 Gly Arg Phe Lys Val Tyr Leu Ile Asp Glu Val His Met LeuSer Arg 50 55 60 His Ser Phe Asn Ala Leu Leu Lys Thr Leu Glu Glu Pro ProGlu His 65 70 75 80 Val Lys Phe Leu Leu Ala Thr Thr Asp Pro Gln Lys LeuPro Val Thr 85 90 95 Ile Leu Ser Arg Cys Leu Gln Phe His Leu Lys Ala LeuAsp Val Glu 100 105 110 Gln Ile Arg His Gln Leu Glu His Ile Leu Asn GluGlu His Ile Ala 115 120 125 His Glu Pro Arg Ala Leu Gln Leu Leu Ala ArgAla Ala Glu Gly Ser 130 135 140 Leu Arg Asp Ala Leu Ser Leu Thr Asp GlnAla Ile Ala Ser Gly Asp 145 150 155 160 Gly Gln Val Ser Thr Gln Ala ValSer Ala Met Leu Gly Thr Leu Asp 165 170 175 Asp Asp Gln Ala 180 665 175PRT Artificial Sequence truncated E. coli delta′ protein 665 His His AlaLeu Leu Ile Gln Ala Leu Pro Gly Met Gly Asp Asp Ala 1 5 10 15 Leu IleTyr Ala Leu Ser Arg Tyr Leu His Pro Asp Tyr Tyr Thr Leu 20 25 30 Ala ProGlu Arg Glu Val Thr Glu Lys Leu Asn Glu His Ala Arg Leu 35 40 45 Gly GlyAla Lys Val Val Trp Val Thr Asp Ala Ala Leu Leu Thr Asp 50 55 60 Ala AlaAla Asn Ala Leu Leu Lys Thr Leu Glu Glu Pro Pro Ala Glu 65 70 75 80 ThrTrp Phe Phe Leu Ala Thr Arg Glu Pro Glu Arg Leu Leu Ala Thr 85 90 95 LeuArg Ser Arg Cys Arg Leu His Tyr Leu Ala Pro Pro Pro Glu Gln 100 105 110Tyr Ala Val Thr Trp Leu Ser Arg Glu Val Thr Met Ser Gln Asp Ala 115 120125 Leu Leu Ala Ala Leu Arg Leu Ser Ala Gly Ser Pro Gly Ala Ala Leu 130135 140 Ala Leu Phe Gln Gly Asp Asn Trp Gln Ala Arg Glu Thr Leu Cys Gln145 150 155 160 Ala Leu Ala Tyr Ser Val Pro Ser Gly Asp Trp Tyr Ser LeuLeu 165 170 175 666 196 PRT Artificial Sequence synthetic truncated E.coli delta protein 666 Arg Ala Ala Tyr Leu Leu Leu Gly Asn Asp Pro LeuLeu Leu Gln Glu 1 5 10 15 Ser Gln Asp Ala Val Arg Gln Val Ala Ala AlaGln Gly Phe Glu Glu 20 25 30 His His Thr Phe Ser Ile Asp Pro Asn Thr AspTrp Asn Ala Ile Phe 35 40 45 Ser Leu Cys Gln Ala Met Ser Leu Phe Ala SerArg Gln Thr Leu Leu 50 55 60 Leu Leu Leu Pro Glu Asn Gly Pro Asn Ala AlaIle Asn Glu Gln Leu 65 70 75 80 Leu Thr Leu Thr Gly Leu Leu His Asp AspLeu Leu Leu Ile Val Arg 85 90 95 Gly Asn Lys Leu Ser Lys Ala Gln Glu AsnAla Ala Trp Phe Thr Ala 100 105 110 Leu Ala Asn Arg Ser Val Gln Val ThrCys Gln Thr Pro Glu Gln Ala 115 120 125 Gln Leu Pro Arg Trp Val Ala AlaArg Ala Lys Gln Leu Asn Leu Glu 130 135 140 Leu Asp Asp Ala Ala Asn GlnVal Leu Cys Tyr Cys Tyr Glu Gly Asn 145 150 155 160 Leu Leu Ala Leu AlaGln Ala Leu Glu Arg Leu Ser Leu Leu Trp Pro 165 170 175 Asp Gly Lys LeuThr Leu Pro Arg Val Glu Gln Ala Val Asn Asp Ala 180 185 190 Ala His PheThr 195 667 185 PRT Artificial Sequence synthetic truncated R.prowazekii delta protein 667 Ile Arg Ala Leu Leu Leu Tyr Gly Pro Asp LysGly Tyr Ile Glu Lys 1 5 10 15 Ile Cys Thr Tyr Leu Ile Lys Asn Leu AsnMet Leu Gln Ser Ser Ile 20 25 30 Glu Tyr Glu Asp Leu Asn Ile Leu Ser LeuAsp Ile Leu Leu Asn Ser 35 40 45 Pro Asn Phe Phe Gly Gln Lys Glu Leu IleLys Val Arg Ser Ile Gly 50 55 60 Asn Ser Leu Asp Lys Asn Leu Lys Thr IleLeu Ser Ser Asp Tyr Ile 65 70 75 80 Asn Phe Pro Val Phe Ile Gly Glu AspMet Asn Ser Ser Gly Ser Val 85 90 95 Lys Lys Phe Phe Glu Thr Glu Glu TyrLeu Ala Val Val Ala Cys Tyr 100 105 110 His Asp Asp Glu Ala Lys Ile GluArg Ile Ile Leu Gly Lys Leu Ala 115 120 125 Lys Thr Asn Lys Val Ile SerLys Glu Ala Ile Thr Tyr Leu Lys Thr 130 135 140 His Leu Lys Gly Asp HisAla Leu Ile Cys Ser Glu Ile Asn Lys Leu 145 150 155 160 Ile Phe Phe AlaHis Asp Val His Glu Ile Thr Leu Asn His Val Leu 165 170 175 Glu Val IleSer Ser Glu Ile Thr Ala 180 185 668 208 PRT Artificial Sequencesynthetic truncated H. pylori delta protein 668 Pro Lys Ala Val Phe LeuTyr Gly Glu Phe Asp Phe Phe Ile His Tyr 1 5 10 15 Tyr Ile Gln Thr IleSer Ala Leu Phe Lys Gly Asn Asn Pro Asp Thr 20 25 30 Glu Thr Ser Leu PheTyr Ala Ser Asp Tyr Glu Lys Ser Gln Ile Ala 35 40 45 Thr Leu Leu Glu GlnAsp Ser Leu Phe Gly Gly Ser Ser Leu Val Ile 50 55 60 Leu Lys Leu Asp PheAla Leu His Lys Lys Phe Lys Glu Asn Asp Ile 65 70 75 80 Asn Pro Phe LeuLys Ala Leu Glu Arg Pro Ser His Asn Arg Leu Ile 85 90 95 Ile Gly Leu TyrAsn Ala Lys Ser Asp Thr Thr Lys Tyr Lys Tyr Thr 100 105 110 Ser Glu IleIle Val Lys Phe Phe Gln Lys Ser Pro Leu Lys Asp Glu 115 120 125 Ala IleCys Val Arg Phe Phe Thr Pro Lys Ala Trp Glu Ser Leu Lys 130 135 140 PheLeu Gln Glu Arg Ala Asn Phe Leu His Leu Asp Ile Ser Gly His 145 150 155160 Leu Leu Asn Ala Leu Phe Glu Ile Asn Asn Glu Asp Leu Ser Val Ser 165170 175 Phe Asn Asp Leu Asp Lys Leu Ala Val Leu Asn Ala Pro Ile Thr Leu180 185 190 Glu Asp Ile Gln Glu Leu Ser Ser Asn Ala Gly Asp Met Asp LeuGln 195 200 205 669 193 PRT Artificial Sequence synthetic truncated M.tuberculosis delta protein 669 Met His Leu Val Leu Gly Asp Glu Glu LeuLeu Val Glu Arg Ala Val 1 5 10 15 Ala Asp Val Leu Arg Ser Ala Arg GlnArg Ala Gly Thr Ala Asp Val 20 25 30 Pro Val Ser Arg Met Arg Ala Gly AspVal Gly Ala Tyr Glu Leu Ala 35 40 45 Glu Leu Leu Ser Pro Ser Leu Phe AlaGlu Glu Arg Ile Val Val Leu 50 55 60 Gly Ala Ala Ala Glu Ala Gly Lys AspAla Ala Ala Val Ile Glu Ser 65 70 75 80 Ala Ala Ala Asp Leu Pro Ala GlyThr Val Leu Val Val Val His Ser 85 90 95 Gly Gly Gly Arg Ala Lys Ser LeuAla Asn Gln Leu Arg Ser Met Gly 100 105 110 Ala Gln Val His Pro Cys AlaArg Ile Thr Lys Val Ser Glu Arg Ala 115 120 125 Asp Phe Ile Arg Ser GluPhe Ala Ser Leu Arg Val Lys Val Asp Asp 130 135 140 Glu Thr Val Thr AlaLeu Leu Asp Ala Val Gly Ser Asp Val Arg Glu 145 150 155 160 Leu Ala SerAla Cys Ser Gln Leu Val Ala Asp Thr Gly Gly Ala Val 165 170 175 Asp AlaAla Ala Val Arg Arg Tyr His Ser Gly Lys Ala Glu Val Arg 180 185 190 Gly670 203 PRT Artificial Sequence synthetic truncated B. subtilis deltaprotein 670 His Pro Val Tyr Cys Leu Tyr Gly Lys Glu Thr Tyr Leu Leu GlnGlu 1 5 10 15 Thr Val Ser Arg Ile Arg Gln Thr Val Val Asp Gln Glu ThrLys Asp 20 25 30 Phe Asn Leu Ser Val Phe Asp Leu Glu Glu Asp Pro Leu AspGln Ala 35 40 45 Ile Ala Asp Ala Glu Thr Phe Pro Phe Met Gly Glu Arg ArgLeu Val 50 55 60 Ile Val Lys Asn Pro Tyr Phe Leu Thr Gly Glu Lys Lys LysGlu Lys 65 70 75 80 Ile Glu His Asn Val Ser Ala Leu Glu Ser Tyr Ile GlnSer Pro Ala 85 90 95 Pro Tyr Thr Val Phe Val Leu Leu Ala Pro Tyr Glu LysLeu Asp Glu 100 105 110 Arg Lys Lys Leu Thr Lys Ala Leu Lys Lys His AlaPhe Met Met Glu 115 120 125 Ala Lys Glu Leu Asn Ala Lys Glu Thr Thr AspPhe Thr Val Asn Leu 130 135 140 Ala Lys Thr Glu Gln Lys Thr Ile Gly ThrGlu Ala Ala Glu His Leu 145 150 155 160 Val Leu Leu Val Asn Gly His LeuSer Ser Ile Phe Gln Glu Ile Gln 165 170 175 Lys Leu Cys Thr Phe Ile GlyAsp Arg Glu Glu Ile Thr Leu Asp Asp 180 185 190 Val Lys Met Leu Val AlaArg Ser Leu Glu Gln 195 200 671 180 PRT Artificial Sequence synthetictruncated M. pneumoniae delta protein 671 Met Thr Val Val Tyr Gly AlaAsp Ile Gly Leu Ile His Gln Gln Leu 1 5 10 15 Asn Gln Leu Leu Asn ProAla Ala Cys Lys Gln Val Trp Phe Gln Asp 20 25 30 Val Asn Lys Leu Tyr AspVal Val Leu Asn Gln Asn Leu Phe Ala Glu 35 40 45 Asp Thr Lys Pro Ile LeuIle His Asn Cys Ser Phe Leu Glu Lys Asn 50 55 60 Asn Leu Thr Lys Ala GluLeu His Cys Leu Lys Thr Leu Lys Asp Thr 65 70 75 80 Asp Val Val Val ThrIle Tyr Ser Asp Ser Pro Ala Asn Ala Leu Ile 85 90 95 Asn Asp Arg Ala IleThr Lys Tyr Ala Cys Lys Pro Val Thr Ala Lys 100 105 110 Thr Ile His GlnVal Ile Ser Lys Ala Ala Lys Thr Leu Lys Leu Asn 115 120 125 Leu Asn ProAsp Leu Ile Asp His Leu Ala Thr Ile Leu Pro Phe Asn 130 135 140 Leu GlyVal Ile Glu Gln Glu Leu Arg Lys Leu Thr Leu Leu Ser Pro 145 150 155 160Ala Glu Leu Gln Asp Lys Lys Met Leu Glu Ala Val Leu Cys Asp Tyr 165 170175 Gln Thr Ser Gln 180 672 174 PRT Artificial Sequence synthetictruncated B. burgdoferi delta protein 672 Gln Ala Val Tyr Leu Leu LeuGly Asn Glu Gln Gly Leu Lys Glu Ala 1 5 10 15 Tyr Leu Lys Glu Leu LeuIle Lys Met Asp Ala Phe Lys Ser Glu Val 20 25 30 Ser Val Thr Lys Ile PheLeu Ser Glu Leu Ser Ala Val Gly Phe Ala 35 40 45 Glu Lys Leu Phe Ser AsnSer Phe Phe Ser Lys Lys Glu Ile Phe Ile 50 55 60 Val Tyr Glu Ser Glu LeuLeu Lys Ala Gly Lys Asp Leu Glu Leu Val 65 70 75 80 Cys Asn Ser Ile LeuLys Ser Asn Asn Lys Thr Val Ile Phe Val Ser 85 90 95 Asn Ser Asn Thr CysAsn Ile Asp Phe Lys Asn Lys Leu Lys Phe Ile 100 105 110 Lys Arg Asn PhePhe Asn Leu Asn Ile Lys Ile Thr Asp Ser Ala Ile 115 120 125 Asn Leu MetLeu Leu Met Leu Asn Ser Asp Thr Lys Ile Leu Lys Phe 130 135 140 Tyr IleAsp Ser Phe Ala Leu Phe Ala Lys Asn Asn Thr Ile Glu Glu 145 150 155 160Glu Asp Ile Ala Ser Trp Ile Ser Phe Ile Arg Phe Glu Asn 165 170 673 193PRT Artificial Sequence synthetic truncated T. pallidum delta protein673 Met Ser Val Trp Leu Phe Thr Gly Pro Glu Ile Gly Glu Arg Asp Ser 1 510 15 Ala Val Gln Glu Val Cys Ala Arg Ala Gln Ala Gln Gly Thr Val Asp 2025 30 Val His Arg Leu Tyr Ala His Glu Thr Pro Val Ala Asp Leu Val Asp 3540 45 Leu Leu Arg Thr Arg Ala Leu Phe Ala Asp Ala Val Cys Val Val Leu 5055 60 Tyr Asn Ala Glu Val Ile Lys Lys Cys Asp Glu Val His Val Leu Thr 6570 75 80 Glu Trp Ile Lys Asp Gly Gly Ser Arg Ala Asp Val Phe Leu Val Leu85 90 95 Ile Ser Asp Ser Val Ser Ile His Lys Arg Ile Glu Gln Asn Ile Ser100 105 110 Pro Val His Lys Arg Val Phe Trp Glu Leu Phe Glu Asn Lys LysHis 115 120 125 Ala Trp Val Gln Arg Phe Phe Phe Gln His Glu Met Arg IleGlu Gln 130 135 140 Glu Ala Ile Glu Ser Leu Leu Glu Leu Val Glu Asn AsnThr Arg Ala 145 150 155 160 Leu Lys Thr Val Cys Thr Gln Leu Ser Leu PhePhe Glu Lys Gly Arg 165 170 175 Arg Ile Thr Ala His Asp Ile Ser Ser LeuLeu Val His Thr Lys Glu 180 185 190 Glu 674 201 PRT Artificial Sequencesynthetic truncated Synechocystis sp. delta protein 674 Met Pro Val TyrPhe Tyr Trp Gly Glu Asp Gln Phe Thr Leu His Gln 1 5 10 15 Ala Val LysGln Leu Gln Lys Arg Cys Leu Asp Pro Gln Trp Glu Ala 20 25 30 Phe Asn PheGlu Lys Ile Pro Gly Glu Gln Ala Asp Ala Thr Gln Arg 35 40 45 Gly Leu GluGln Ala Leu Thr Pro Pro Phe Gly Ser Gly Asp Arg Leu 50 55 60 Val Trp ValVal Asp Ser Thr Leu Gly Gln Ser Cys Asp Asp Gly Leu 65 70 75 80 Leu AlaArg Leu Gln Lys Ser Leu Pro Ala Ile Pro Thr Asp Cys His 85 90 95 Leu LeuPhe Thr Ser Ser Lys Lys Leu Asp Arg Arg Leu Lys Ser Thr 100 105 110 LysTyr Leu Glu Gly Asn Ala Thr Ile Arg Glu Phe Ala Leu Ile Ser 115 120 125Pro Trp Asn Val Asp Ala Leu Ile His Gln Ile Gln Ala Ile Ala Gln 130 135140 Asp Leu Gln Leu Pro Leu Ala Thr Glu Thr Glu Gly Phe Leu Ala Glu 145150 155 160 Ala Leu Gly Asn Asp Thr Arg Leu Ile Trp Asn Glu Leu Gly LysLeu 165 170 175 Lys Leu Tyr Ser Glu Ser Gln Thr Gly Pro Leu Thr Val AlaGln Val 180 185 190 Glu Gln Leu Val Asn Thr Ser Thr Gln 195 200 675 189PRT Artificial Sequence synthetic truncated C. pneumoniae delta protein675 Val Pro Ala Ile Ala Leu Ile Gly Ser Ala Leu Glu Asp Asp Lys Asp 1 510 15 Ala Leu Ile Glu Leu Leu Val Ser Glu Ser Phe Lys Glu Leu Gly Gly 2025 30 Gln Gly Leu Met Pro Ala Thr Leu Met Ser Trp Thr Glu Thr Phe Ala 3540 45 Leu Phe Gln Glu His Glu Thr Leu Gly Ile Ile His Ala Glu Lys Phe 5055 60 Pro Leu Ala Thr Lys Glu Phe Leu Ser Arg Tyr Ala Arg Asn Pro Gln 6570 75 80 Pro His Leu Thr Ile Leu Ile Phe Thr Thr Lys Gln Glu Cys Phe Arg85 90 95 Glu Leu Ser Lys Ala Leu Pro Ser Ala Leu Ser Leu Ser Leu Phe Gly100 105 110 Glu Trp Pro Ala Asp Arg Gln Lys Arg Ile Ile Arg Leu Leu LeuGln 115 120 125 Arg Ala Glu Arg Val Gly Ile Ser Cys Ser Gln Ser Leu AlaSer Leu 130 135 140 Phe Leu Arg Ala Leu Ala Ser Thr Ser Leu Pro Asp IleLeu Ser Glu 145 150 155 160 Phe Asp Lys Leu Leu Cys Ser Val Gly Lys LysThr Ser Leu Asp His 165 170 175 Ser Asp Ile Lys Glu Leu Val Val Lys LysGlu Lys Ala 180 185 676 181 PRT Artificial Sequence synthetic truncatedD. radiodurans delta protein 676 Met Pro Val Leu Ala Phe Thr Gly Asn ArgPhe Leu Ala Asp Glu Thr 1 5 10 15 Leu Arg Asp Thr Leu Ser Ala Arg GlyLeu Asn Ala Arg Asp Leu Pro 20 25 30 Arg Phe Ser Gly Glu Asp Val Ser AlaGlu Thr Leu Gly Pro His Leu 35 40 45 Ala Pro Ser Leu Phe Gly Asp Gly GlyVal Val Val Asp Phe Glu Gly 50 55 60 Leu Lys Pro Asp Lys Ala Leu Leu GluLeu Leu Ser Ser Ala Pro Val 65 70 75 80 Thr Val Ala Val Leu Asp Glu AlaPro Pro Ala Thr Arg Leu Lys Leu 85 90 95 Tyr Gln Lys Ala Gly Glu Val IlePro Ser Ala Ala Pro Ser Lys Pro 100 105 110 Gly Asp Val Thr Gly Trp ValVal Thr Arg Ala Lys Lys Met Gly Leu 115 120 125 Arg Leu Glu Arg Asp AlaAla Ser Tyr Leu Ala Glu Val Phe Gly Ala 130 135 140 Asp Leu Ala Gly IleAla Gly Glu Leu Asn Lys Leu Glu Leu Leu Gly 145 150 155 160 Gly Ala LeuAsn Arg Glu Arg Val Gln Gly Ile Val Gly Arg Asp Pro 165 170 175 Pro GlyAsp Ser Phe 180 677 179 PRT Artificial Sequence synthetic truncated T.maritima delta protein 677 Met Pro Val Thr Phe Leu Thr Gly Thr Ala GluThr Gln Lys Glu Glu 1 5 10 15 Leu Ile Lys Lys Leu Leu Lys Asp Gly AsnVal Glu Tyr Ile Arg Ile 20 25 30 His Pro Glu Asp Pro Asp Lys Ile Asp PheIle Arg Ser Leu Leu Arg 35 40 45 Thr Lys Thr Ile Phe Ser Asn Lys Thr IleIle Asp Ile Val Asn Phe 50 55 60 Asp Glu Trp Lys Ala Gln Glu Gln Lys ArgLeu Val Glu Leu Leu Lys 65 70 75 80 Asn Val Pro Glu Asp Val His Ile PheIle Arg Ser Gln Lys Thr Gly 85 90 95 Gly Lys Gly Val Ala Leu Glu Leu ProLys Pro Trp Glu Thr Asp Lys 100 105 110 Trp Leu Glu Trp Ile Glu Lys ArgPhe Arg Glu Asn Gly Leu Leu Ile 115 120 125 Asp Lys Asp Ala Leu Gln LeuPhe Phe Ser Lys Val Gly Thr Asn Asp 130 135 140 Leu Ile Ile Glu Arg GluIle Glu Lys Leu Lys Ala Tyr Ser Glu Asp 145 150 155 160 Arg Lys Ile ThrVal Glu Asp Val Glu Glu Val Val Phe Thr Tyr Gln 165 170 175 Thr Pro Gly678 198 PRT Artificial Sequence synthetic truncated A. aeolicus deltaprotein 678 Glu Arg Val Phe Val Leu His Gly Glu Glu Gln Tyr Leu Ile ArgThr 1 5 10 15 Phe Leu Ser Lys Leu Lys Glu Lys Tyr Gly Glu Asn Tyr ThrVal Leu 20 25 30 Trp Gly Asp Glu Ile Ser Glu Glu Glu Phe Tyr Thr Ala LeuSer Glu 35 40 45 Thr Ser Ile Phe Gly Gly Ser Lys Glu Lys Ala Val Val IleTyr Asn 50 55 60 Phe Gly Asp Phe Leu Lys Lys Leu Gly Arg Lys Lys Lys GluLys Glu 65 70 75 80 Arg Leu Ile Lys Val Leu Arg Asn Val Lys Ser Asn TyrVal Phe Ile 85 90 95 Val Tyr Asp Ala Lys Leu Gln Lys Gln Glu Leu Ser SerGlu Pro Leu 100 105 110 Lys Ser Val Ala Ser Phe Gly Gly Ile Val Val AlaAsn Arg Leu Ser 115 120 125 Lys Glu Arg Ile Lys Gln Leu Val Leu Lys LysPhe Lys Glu Lys Gly 130 135 140 Ile Asn Val Glu Asn Asp Ala Leu Glu TyrLeu Leu Gln Leu Thr Gly 145 150 155 160 Tyr Asn Leu Met Glu Leu Lys LeuGlu Val Glu Lys Leu Ile Asp Tyr 165 170 175 Ala Ser Glu Lys Lys Ile LeuThr Leu Asp Glu Val Lys Arg Val Ala 180 185 190 Phe Ser Val Ser Glu Asn195

1. A method of identifying a modulator of the interaction between the βsubunit of a eubacterial DNA polymerase III (β protein) and proteinsthat interact therewith by binding at a surface of said β proteindefined by the residues X¹⁷⁰, X¹⁷², X¹⁷⁵, X¹⁷⁷, X²⁴¹, X²⁴², X²⁴⁷, X³⁴⁶,X³⁶⁰ and X³⁶², wherein the superscript numbers designate the position ofresidues in Escherichia coli β protein, or the equivalent residues inhomologues from other species of eubacteria, and wherein: X¹⁷⁰ is anyone of V, I, A, T, S or E; X¹⁷² is any one of T, S or I; X¹⁷⁵ is any oneof H, Y, F, K, I, Q or R; X¹⁷⁷ is any one of L, M, I, F, V or A; X²⁴¹ isany one of F, Y or L; X²⁴² is any one of P, L or I; X²⁴⁷ is any one ofV, I, A, F, L or M; X³⁴⁶ is any one of S, P, A, Y or K; X³⁶⁰ is any oneof I, L or V; and X³⁶² is any one of M, L, V, S, T or R; wherein saidmethod comprises the steps of: (a) forming a reaction mixturecomprising: (i) a ligand for eubacterial β protein that binds to atleast part of said surface of β protein; (ii) an interaction partner forsaid ligand; and (iii) a test compound; (b) incubating said reactionmixture under conditions which in the absence of said test compoundallow interaction between said ligand and said interaction partner; and(c) assessing the effect of said test compound on said interactionbetween said ligand and said interaction partner.
 2. The methodaccording to claim 1, wherein said ligand is selected from the groupconsisting of a protein, a peptide, an antibody, and a mimetic of saidpeptide.
 3. The method according to claim 2, wherein said protein isselected from the group consisting of δ, DnaE1, DnaE2, PolC, PolB2,UmuC, DinB1, DinB2, DinB3, MutS1, RepA, Duf72 and DnaA2, and fragmentsthereof that bind to at least part of said surface of β protein.
 4. Themethod according to claim 2, wherein said protein is selected from afragment of δ, DnaE1, DnaE2, PolC, PolB2, UmuC, DinB1, DinB2, DinB3,MutS1, RepA, Duf72 and DnaA2 that binds to at least part of said surfaceof β protein, which fragment is fused to another protein.
 5. The methodaccording to claim 2, wherein said peptide selected from the groupconsisting of X¹X², X³X¹X², X³X¹X²X⁴, QX⁵X³X¹X², and QX⁵xX⁶X³X⁶,wherein: x is any amino acid residue; X¹ is L, M, I, or F; X² is L, I,V, C, F, Y, W, P, D, A or G; X³ is A, G, T, N, D, S, or P; X⁴ is A or G;X⁵ is L; and, X⁶ is L, I, V, C, F, Y, W or P.
 6. The method according toclaim 2, wherein said ligand is a polypeptide or peptide that includes asequence selected from the group consisting of X¹X², X³X¹X², X³X¹X²X⁴,QX⁵X³X¹X², and QX⁵xX⁶X³X⁶, wherein: x is any amino acid residue; X¹ isL, M, I, or F; X² is L, I, V, C, F, Y, W, P, D, A or G; X³ is A, G, T,N, D, S, or P; X⁴ is A or G; X⁵ is L; and, X⁶ is L, I, V, C, F, Y, W orP.
 7. The method according to claim 2, wherein said ligand is apolypeptide or peptide that includes any one of the motifs of Tables 1to 13 and 15, or is a peptide comprising any one of the motifs of Tables1 to 13 and
 15. 8. The method according to claim 2, wherein saidinteraction partner is selected from the group consisting of eubacterialβ protein, a fragment of eubacterial β protein that includes at least afunctional portion of said surface of β protein, and a mimetic of saidsurface of β protein.
 9. A method for the in vivo identification of amodulator of the interaction between the β subunit of a eubacterial DNApolymerase III (β protein) and proteins that interact therewith bybinding at a surface of said β protein defined by the residues X¹⁷⁰,X¹⁷², X¹⁷⁵, X¹⁷⁷, X²⁴¹, X²⁴², X²⁴⁷, X³⁴⁶, X³⁶⁰ and X³⁶², wherein thesuperscript numbers designate the position of residues in Escherichiacoli β protein, or the equivalent residues in homologues from otherspecies of eubacteria, and wherein: X¹⁷⁰ is any one of V, I, A, T, S orE; X¹⁷² is any one of T, S or I; X¹⁷⁵ is any one of H, Y, F, K, I, Q orR; X¹⁷⁷ is any one of L, M, I, F, V or A; X²⁴¹ is any one of F, Y or L;X²⁴² is any one of P, L or I; X²⁴⁷ is any one of V, I, A, F, L or M;X³⁴⁶ is any one of S, P, A, Y or K; X³⁶⁰ is any one of I, L or V; andX³⁶² is any one of M, L, V, S, T or R; wherein said method comprises thesteps of: (a) modifying a host to express or contain: (i) a ligand foreubacterial β protein that binds to at least part of said surface of βprotein; and (ii) an interaction partner for said ligand; (b)administering a test compound to said host and incubating the host underconditions which in the absence of said test compound allows interactionbetween said ligand and said interaction partner; and (c) assessing theeffect of said test compound on said interaction between said ligand andsaid interaction partner.
 10. The method according to claim 9, whereinsaid host is selected from the group consisting of animal cells, plantcells, fungal cells, bacterial cells, bacteriophages and viruses. 11.The method according to claim 9, wherein said ligand is a proteinselected from the group consisting of δ, DnaE1, DnaE2, PolC, PolB2,UmuC, DinB1, DinB2, DinB3, MutS1, RepA, Duf72 and DnaA2, and fragmentsthereof that bind to at least part of said surface of β protein.
 12. Themethod according to claim 9, wherein said ligand is a peptide selectedfrom the group consisting of X¹X², X³X¹X², X³X¹X²X⁴, QX⁵X³X¹X², andQX⁵xX⁶X³X⁶, wherein: x is any amino acid residue; X¹ is L, M, I, or F;X² is L, I, V, C, F, Y, W, P, D, A or G; X³ is A, G, T, N, D, S, or P;X⁴ is A or G; X⁵ is L; and, X⁶ is L, I, V, C, F, Y, W or P.
 13. Themethod according to claim 9, wherein said ligand is a polypeptide orpeptide that includes a sequence selected from the group consisting ofX¹X², X³X¹X², X³X¹X²X⁴, QX⁵X³X¹X², and QX⁵xX⁶X³X⁶, wherein: x is anyamino acid residue; X¹ is L, M, I, or F; X² is L, I, V, C, F, Y, W, P,D, A or G; X³ is A, G, T, N, D, S, or P; X⁴ is A or G; X⁵ is L; and, X⁶is L, I, V, C, F, Y, W or P.
 14. The method according to claim 9,wherein said ligand is a polypeptide or peptide that includes any one ofthe motifs of Tables 1 to 13 and 15, or is a peptide comprising any oneof the motifs of Tables 1 to 13 and
 15. 15. The method according toclaim 9, wherein said interaction partner is selected from the groupconsisting of eubacterial β protein, and a fragment of eubacterial βprotein that includes at least a functional portion of said surface of βprotein.
 16. A method of selecting a potential modulator of theinteraction between the β subunit of a eubacterial DNA polymerase III (βprotein) and proteins that interact therewith by binding at a surface ofsaid β protein defined by the residues X¹⁷⁰, X¹⁷², X¹⁷⁵, X¹⁷⁷, X²⁴¹,X²⁴², X²⁴⁷, X³⁴⁶, X³⁶⁰ and X³⁶², wherein the superscript numbersdesignate the position of residues in Escherichia coli β protein, or theequivalent residues in homologues from other species of eubacteria, andwherein: X¹⁷⁰ is any one of V, I, A, T, S or E; X¹⁷² is any one of T, Sor I; X¹⁷⁵ is any one of H, Y, F, K, I, Q or R; X¹⁷⁷ is any one of L, M,I, F, V or A; X²⁴¹ is any one of F, Y or L; X²⁴² is any one of P, L orI; X²⁴⁷ is any one of V, I, A, F, L or M; X³⁴⁶ is any one of S, P, A, Yor K; X³⁶⁰ is any one of I, L or V; and X³⁶² is any one of M, L, V, S, Tor R; wherein said method comprises the steps of: (a) establishing aconsensus sequence for peptides that bind to at least part of saidsurface of β protein; (b) modelling the structure of at least a portionof said consensus sequence and searching compound databases forcompounds having a similar structure; wherein said modelling is by: (i)searching protein databases for occurrences of said consensus sequenceor portion thereof, obtaining coordinates of residues of proteinscomprising said consensus sequence or portion thereof, and superimposingsaid coordinates to produce a pharmacophore model; or (ii) modelling ordetermining the structure of a peptide including said consensus sequenceor a portion thereof when bound to β protein; and (c) testing compoundsidentified in step (b) for their effect on said interaction.
 17. Themethod according to claim 16, wherein said consensus sequence isselected from the sequence data of any one of Tables 1 to 13 and
 15. 18.A method of reducing the effect of eubacterial infestation of abiological system, the method comprising delivering to a system infestedwith a eubacterial species a modulator of the interaction between the βsubunit of eubacterial DNA polymerase III (β protein)and proteins thatinteract therewith by binding at a surface of said β protein defined bythe residues X¹⁷⁰, X¹⁷², X¹⁷⁵, X¹⁷⁷, X²⁴¹, X²⁴², X²⁴⁷, X³⁴⁶, X³⁶⁰ andX³⁶², wherein the superscript numbers designate the position of residuesin Escherichia coli β protein, or the equivalent residues in homologuesfrom other species of eubacteria, and wherein: X¹⁷⁰ is any one of V, I,A, T, S or E; X¹⁷² is any one of T, S or I; X¹⁷⁵ is any one of H, Y, F,K, I, Q or R; X¹⁷⁷ is any one of L, M, I, F, V or A; X²⁴¹ is any one ofF, Y or L; X²⁴² is any one of P, L or I; X²⁴⁷ is any one of V, I, A, F,L or M; X³⁴⁶ is any one of S, P, A, Y or K; X³⁶⁰ is any one of I, L orV; and X³⁶² is any one of M, L, V, S, T or R.
 19. The method accordingto claim 18, wherein said modulator is a peptide selected from the groupconsisting of X¹X², X³X¹X², X³X¹X²X⁴, QX⁵X³X¹X², and QX⁵xX⁶X³X⁶,wherein: X is any amino acid residue; X¹ is L, M, I, or F; X² is L, I,V, C, F, Y, W, P, D, A or G; X³ is A, G, T, N, D, S, or P; X⁴ is A or G;X⁵ is L; and, X⁶ is L, I, V, C, F, Y, W or P.
 20. The method accordingto claim 18, wherein said modulator is a mimetic of any one of thepeptides defined in claim
 19. 21. The method according to claim 18,wherein said modulator is an inhibitor of the interaction betweeneubacterial β protein and proteins that interact therewith.
 22. A methodof selecting a potential modulator of the interaction between the βsubunit of a eubacterial DNA polymerase III (β protein) and proteinsthat interact therewith by binding at a surface of said β proteindefined by the residues X¹⁷⁰, X¹⁷², X¹⁷⁵, X¹⁷⁷, X²⁴¹, X²⁴², X²⁴⁷, X³⁴⁶,X³⁶⁰ and X³⁶², wherein the superscript numbers designate the position ofresidues in Escherichia coli β protein, or the equivalent residues inhomologues from other species of eubacteria, and wherein: X¹⁷⁰ is anyone of V, I, A, T, S or E; X¹⁷² is any one of T, S or I; X¹⁷⁵ is any oneof H, Y, F, K, I, Q or R; X¹⁷⁷ is any one of L, M, I, F, V or A; X²⁴¹ isany one of F, Y or L; X⁴² is any one of P, L or I; X²⁴⁷ is any one of V,I, A, F, L or M; X³⁴⁶ is any one of S, P, A, Y or K; X³⁶⁰ is any one ofI, L or V; and X³⁶² is any one of M, L, V, S, T or R; wherein saidmethod comprises the steps of: (a) designing a mimetic of a peptideselected from the group consisting of X¹X², X³X¹X², X³X¹X²X⁴, QX⁵X³X¹X²,and QX⁵xX⁶X³X⁶, wherein: x is any amino acid residue; X¹ is L, M, I, orF; X² is L, I, V, C, F, Y, W, P, D, A or G; X³ is A, G, T, N, D, S, orP; X⁴ is A or G; X⁵ is L; and, X⁶ is L, I, V, C, F, Y, W or P; (b)testing said mimetic for its effect on said interaction.
 23. The methodaccording to claim 22, wherein said peptide is selected from the groupconsisting of: QLSLF (Seq. ID No. 622); QLSMF (Seq. ID No. 623); QLDMF(Seq. ID No. 624); QLDLF (Seq. ID No. 625); HLSLF (Seq. ID No. 626);HLSMF (Seq. ID No. 627); HLDMF (Seq. ID No. 628); HLDLF (Seq. ID No.629); X³LFX⁴; SLF; SMF; DLF; DMF; LF; and MF.
 24. The method accordingto claim 22, wherein said peptide is any one of the motifs of Tables 1to 13 and 15.